diff --git a/LifeSciences/AzureBlast/AzureBlast.Web/Controllers/Api/SearchesController.cs b/LifeSciences/AzureBlast/AzureBlast.Web/Controllers/Api/SearchesController.cs
index 98eab94..ad78480 100644
--- a/LifeSciences/AzureBlast/AzureBlast.Web/Controllers/Api/SearchesController.cs
+++ b/LifeSciences/AzureBlast/AzureBlast.Web/Controllers/Api/SearchesController.cs
@@ -42,9 +42,9 @@ namespace Microsoft.Azure.Blast.Web.Controllers.Api
         }
 
         [Route("searches/{searchId}/queries"), HttpGet]
-        public IEnumerable<SearchQuery> GetSearchQueries(Guid searchId)
+        public IEnumerable<SearchQueryEntity> GetSearchQueries(Guid searchId)
         {
-            return _searchProvider.ListSearchQueries(searchId).OrderBy(q => q.InputFilename);
+            return _searchProvider.ListSearchQueries(searchId).OrderBy(q => q.QueryFilename);
         }
 
         [Route("searches/{searchId}"), HttpGet]
@@ -116,13 +116,89 @@ namespace Microsoft.Azure.Blast.Web.Controllers.Api
 
                     using (var reader = fileInfo.OpenText())
                     {
-                        var sequenceText = reader.ReadToEnd();
-                        searchInputFiles.Add(new SearchInputFile
+                        var fullFilename = file.Headers.ContentDisposition.FileName.Replace("\"", "");
+
+                        if (searchModel.SplitSequenceFile)
                         {
-                            Filename = file.Headers.ContentDisposition.FileName.Replace("\"", ""),
-                            Length = fileInfo.Length,
-                            Content = new MemoryStream(Encoding.UTF8.GetBytes(sequenceText)),
-                        });
+                            var filename = Path.GetFileNameWithoutExtension(fullFilename);
+                            var extension = Path.GetExtension(fullFilename);
+
+                            int currentSequenceCount = 0;
+                            int currentFileCount = 1;
+                            string currentSequenceContent = null;
+                            string sequenceFilename;
+
+                            var line = reader.ReadLine();
+                            while (line != null)
+                            {
+                                if (string.IsNullOrEmpty(line) || line.Trim() == "")
+                                {
+                                    continue;
+                                }
+
+                                if (line.StartsWith(">"))
+                                {
+                                    if (string.IsNullOrEmpty(currentSequenceContent))
+                                    {
+                                        // We're the first sequence
+                                        currentSequenceContent = line;
+                                    }
+                                    else
+                                    {
+                                        currentSequenceCount++;
+
+                                        if (currentSequenceCount % searchModel.SequencesPerQuery == 0)
+                                        {
+                                            // Flush previous sequence(s)
+                                            sequenceFilename = string.Format("{0}_part{1}{2}",
+                                                filename, currentFileCount++, extension);
+                                            searchInputFiles.Add(new SearchInputFile
+                                            {
+                                                Filename = sequenceFilename,
+                                                Length = Encoding.UTF8.GetByteCount(currentSequenceContent),
+                                                Content = new MemoryStream(Encoding.UTF8.GetBytes(currentSequenceContent)),
+                                            });
+
+                                            currentSequenceContent = line;
+                                        }
+                                        else
+                                        {
+                                            // Keep appending
+                                            currentSequenceContent += "\n" + line;
+                                        }
+                                    }
+                                }
+                                else
+                                {
+                                    currentSequenceContent += "\n" + line;
+                                }
+
+                                line = reader.ReadLine();
+                            }
+
+                            if (!string.IsNullOrEmpty(currentSequenceContent))
+                            {
+                                // Flush the final one
+                                sequenceFilename = string.Format("{0}_part{1}{2}",
+                                    filename, currentFileCount, extension);
+                                searchInputFiles.Add(new SearchInputFile
+                                {
+                                    Filename = sequenceFilename,
+                                    Length = Encoding.UTF8.GetByteCount(currentSequenceContent),
+                                    Content = new MemoryStream(Encoding.UTF8.GetBytes(currentSequenceContent)),
+                                });
+                            }
+                        }
+                        else
+                        {
+                            var sequenceText = reader.ReadToEnd();
+                            searchInputFiles.Add(new SearchInputFile
+                            {
+                                Filename = fullFilename,
+                                Length = fileInfo.Length,
+                                Content = new MemoryStream(Encoding.UTF8.GetBytes(sequenceText)),
+                            });
+                        }
                     }
 
                     try
@@ -157,6 +233,12 @@ namespace Microsoft.Azure.Blast.Web.Controllers.Api
                         "The program name must be provided with the search");
                 }
 
+                if (searchModel.SplitSequenceFile && searchModel.SequencesPerQuery < 1)
+                {
+                    return Request.CreateErrorResponse(HttpStatusCode.BadRequest,
+                        "Sequences per query must ne greater than 0 when splitting a sequence file.");
+                }
+
                 if (!searchModel.SearchInputFiles.Any())
                 {
                     return Request.CreateErrorResponse(HttpStatusCode.BadRequest,
@@ -191,6 +273,8 @@ namespace Microsoft.Azure.Blast.Web.Controllers.Api
                 Executable = formData["executable"],
                 ExecutableArgs = formData["executableArgs"],
                 SearchInputFiles = new List<SearchInputFile>(),
+                SplitSequenceFile = ToBoolean(formData["splitSequenceFile"]),
+                SequencesPerQuery = ToInt(formData["seqencesPerQuery"], 1),
             };
 
             AddPoolSpecToSearch(formData, spec);
@@ -231,5 +315,25 @@ namespace Microsoft.Azure.Blast.Web.Controllers.Api
                 spec.PoolDisplayName = formData["poolName"];
             }
         }
+
+        private bool ToBoolean(string formValue)
+        {
+            bool value;
+            if (Boolean.TryParse(formValue, out value))
+            {
+                return value;
+            }
+            return false;
+        }
+
+        private int ToInt(string formValue, int defaultValue)
+        {
+            int value;
+            if (int.TryParse(formValue, out value))
+            {
+                return value;
+            }
+            return defaultValue;
+        }
     }
 }
diff --git a/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/New.cshtml b/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/New.cshtml
index f89b7d3..7710af8 100644
--- a/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/New.cshtml
+++ b/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/New.cshtml
@@ -54,7 +54,19 @@
             <div class="form-group">
                 <label class="control-label col-sm-2" for="searchFile">Sequence file(s)</label>
                 <div class="col-sm-10">
-                    <input id="searchFile" name="searchFile" type="file" multiple="multiple" accept="*" />
+                    <input id="searchFile" name="searchFile" type="file" multiple="multiple" accept="*"/>
+                </div>
+            </div>
+            <div class="form-group">
+                <label class="control-label col-sm-2" for="searchFile">Split sequence file</label>
+                <div class="col-sm-10">
+                    <input id="splitSequenceFileCheckBox" type="checkbox" name="splitSequenceFile" value="0">
+                </div>
+            </div>
+            <div class="form-group">
+                <label class="control-label col-sm-2" for="seqencesPerQuery">Sequences per query</label>
+                <div class="col-sm-10">
+                    <input id="seqencesPerQuery" type="text" class="form-control" placeholder="1" aria-describedby="basic-addon1" value="1">
                 </div>
             </div>
         </div>
@@ -235,6 +247,9 @@
 
                 var searchName = $('#searchName').val().trim();
                 var searchSequenceText = $('#searchSequenceText').val().trim();
+                var splitSequenceFile = $('#splitSequenceFileCheckBox').is(':checked');
+                var seqencesPerQuery = $('#seqencesPerQuery').val().trim();
+
 
                 var poolId = $('#poolListBtn').text().trim();
                 var vmSize = $('#vmSizeListBtn').text().trim();
@@ -245,6 +260,8 @@
                 var searchFile = $("#searchFile")[0];
                 formData.append("searchName", searchName);
                 formData.append("searchSequenceText", searchSequenceText);
+                formData.append("splitSequenceFile", splitSequenceFile);
+                formData.append("seqencesPerQuery", seqencesPerQuery);
                 formData.append("databaseName", database);
                 formData.append("executable", executable);
                 formData.append("executableArgs", executableArgs);
diff --git a/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/Show.cshtml b/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/Show.cshtml
index 1cfdbd8..6f5a1e9 100644
--- a/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/Show.cshtml
+++ b/LifeSciences/AzureBlast/AzureBlast.Web/Views/Searches/Show.cshtml
@@ -116,7 +116,7 @@
 {
     <script id="query-template" type="text/x-handlebars-template">
         <tr>
-            <td>{{inputFilename}}</td>
+            <td>{{queryFilename}}</td>
             <td>{{state}}</td>
             <td>{{startTimeFormatted}}</td>
             <td>{{endTimeFormatted}}</td>
diff --git a/LifeSciences/AzureBlast/AzureBlast/AzureBlast.csproj b/LifeSciences/AzureBlast/AzureBlast/AzureBlast.csproj
index d18d381..18350ad 100644
--- a/LifeSciences/AzureBlast/AzureBlast/AzureBlast.csproj
+++ b/LifeSciences/AzureBlast/AzureBlast/AzureBlast.csproj
@@ -157,10 +157,10 @@
     <Compile Include="Searches\QueryState.cs" />
     <Compile Include="Searches\Search.cs" />
     <Compile Include="Searches\SearchInputFile.cs" />
-    <Compile Include="Searches\SearchQuery.cs" />
     <Compile Include="Searches\SearchSpecification.cs" />
     <Compile Include="Searches\SearchState.cs" />
     <Compile Include="Searches\TimeSpanExtensions.cs" />
+    <Compile Include="Storage\Entities\SearchQueryEntity.cs" />
     <Compile Include="Storage\InputFileStager.cs" />
     <Compile Include="Storage\RenewableBlobLease.cs" />
     <Compile Include="Storage\AzureBlobStorageProvider.cs" />
@@ -189,6 +189,9 @@
     <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
+    <Content Include="BatchScripts\SearchJobManager.py">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </Content>
     <Content Include="BatchScripts\jobmanager.py">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </Content>
diff --git a/LifeSciences/AzureBlast/AzureBlast/BatchScripts/SearchJobManager.py b/LifeSciences/AzureBlast/AzureBlast/BatchScripts/SearchJobManager.py
new file mode 100644
index 0000000..e5046b2
--- /dev/null
+++ b/LifeSciences/AzureBlast/AzureBlast/BatchScripts/SearchJobManager.py
@@ -0,0 +1,119 @@
+import os
+import sys
+import datetime
+import time
+import azure.batch.batch_service_client as batch
+import azure.batch.batch_auth as batchauth
+import azure.batch.models as batchmodels
+from azure.storage.table import TableService, TableBatch
+from azure.storage.blob import BlockBlobService
+
+
+def get_search_state(all_tasks_complete, any_failures):
+    if all_tasks_complete and any_failures:
+        return 'Error'
+    if all_tasks_complete:
+        return 'Complete'
+    return 'Running'
+
+
+def get_query_state(task):
+    if task.state == batchmodels.TaskState.active:
+        return 'Waiting'
+    if task.state == batchmodels.TaskState.preparing:
+        return 'Waiting'
+    if task.state == batchmodels.TaskState.running:
+        return 'Running'
+    if task.state == batchmodels.TaskState.completed:
+        if task.execution_info.exit_code == 0:
+            return 'Success'
+        return 'Error'
+
+def wait_for_tasks_to_complete(
+        table_service, batch_client, entity_pk, entity_rk, job_id):
+    """
+    Returns when all tasks in the specified job reach the Completed state.
+    """
+
+    while True:
+        entity = table_service.get_entity(
+            'SearchEntity', entity_pk, entity_rk)
+
+        tasks = batch_client.task.list(job_id)
+
+        incomplete_tasks = [task for task in tasks if
+                            task.id != 'JobManager' and
+                            task.state != batchmodels.TaskState.completed]
+        complete_tasks = [task for task in tasks if
+                            task.id != 'JobManager' and
+                            task.state == batchmodels.TaskState.completed]
+        failed_tasks = [task for task in complete_tasks if
+                            task.execution_info.exit_code != 0 or
+                            task.execution_info.scheduling_error is not None]
+
+        queries = table_service.query_entities(
+            'SearchQueryEntity',
+            filter="PartitionKey eq '{}'".format(entity.RowKey))
+
+        updateBatch = TableBatch()
+
+        for task in tasks:
+            matching_queries = [q for q in queries if q.RowKey == task.id]
+            if not matching_queries:
+                print('Could not find query {}'.format(task.id))
+                continue
+            query = matching_queries[0]
+            update = False
+            state = get_query_state(task)
+            if query._State != state:
+                query._State = state
+                update = True
+
+            if task.state == batchmodels.TaskState.running:
+                if not hasattr(query, 'StartTime'):
+                    query.StartTime = task.execution_info.start_time
+                    update = True
+
+            if task.state == batchmodels.TaskState.completed:
+                if not hasattr(query, 'EndTime'):
+                    query.EndTime = task.execution_info.end_time
+                    update = True
+
+            if update:
+                updateBatch.update_entity(query)
+
+        table_service.commit_batch('SearchQueryEntity', updateBatch)
+
+        all_tasks_complete = not incomplete_tasks
+        any_failures = len(failed_tasks) > 0
+
+        entity.CompletedTasks = len(complete_tasks)
+        entity._State = get_search_state(all_tasks_complete, any_failures)
+
+        if not incomplete_tasks:
+            entity.EndTime = datetime.datetime.utcnow()
+            table_service.update_entity('SearchEntity', entity)
+            return
+        else:
+            table_service.update_entity('SearchEntity', entity)
+            time.sleep(5)
+
+
+if __name__ == '__main__':
+    storage_account = sys.argv[1]
+    storage_key = sys.argv[2]
+    batch_account = sys.argv[3]
+    batch_key = sys.argv[4]
+    batch_url = sys.argv[5]
+    job_id = sys.argv[6]
+    entity_pk = sys.argv[7]
+    entity_rk = sys.argv[8]
+
+    table_service = TableService(account_name=storage_account,
+                                 account_key=storage_key)
+    blob_service = BlockBlobService(account_name=storage_account,
+                                 account_key=storage_key)
+    credentials = batchauth.SharedKeyCredentials(batch_account, batch_key)
+    batch_client = batch.BatchServiceClient(credentials, base_url=batch_url)
+    wait_for_tasks_to_complete(table_service, batch_client, entity_pk, entity_rk, job_id)
+
diff --git a/LifeSciences/AzureBlast/AzureBlast/Searches/AzureSearchProvider.cs b/LifeSciences/AzureBlast/AzureBlast/Searches/AzureSearchProvider.cs
index 69b9d03..db6e5f6 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Searches/AzureSearchProvider.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Searches/AzureSearchProvider.cs
@@ -68,13 +68,25 @@ namespace Microsoft.Azure.Batch.Blast.Searches
                     _blobStorageProvider.UploadBlobFromStream(searchEntity.InputContainer, filename, queryFile.Content);
                 });
 
-                // Keep record of the filenames
-                searchEntity.Files =
-                    search.SearchInputFiles.Select(queryFile => Path.GetFileName(queryFile.Filename)).ToList();
+                var queryIndex = 0;
+                var searchQueries = new List<SearchQueryEntity>();
+                foreach (var queryFile in search.SearchInputFiles)
+                {
+                    var query = new SearchQueryEntity(searchEntity.Id, queryIndex.ToString());
+                    query.OutputContainer = searchEntity.OutputContainer;
+                    query.QueryFilename = Path.GetFileName(queryFile.Filename);
+                    query.State = QueryState.Waiting;
+                    query.QueryOutputFilename = GetQueryOutputFilename(searchEntity.OutputfileFormat, queryIndex.ToString());
+                    query.LogOutputFilename = GetLogFilename(searchEntity.OutputfileFormat, queryIndex.ToString());
+                    searchQueries.Add(query);
+                    queryIndex++;
+                }
+
+                _tableStorageProvider.InsertEntities(searchQueries);
 
                 // Stage the generic batch scripts to storage
                 var resourceFiles = InputFileStager.StageImportScripts(_blobStorageProvider);
-                SubmitBatchJob(searchEntity, resourceFiles);
+                SubmitBatchJob(searchEntity, searchQueries, resourceFiles);
 
                 searchEntity.State = SearchState.Running;
                 _tableStorageProvider.UpdateEntity(searchEntity);
@@ -143,7 +155,7 @@ namespace Microsoft.Azure.Batch.Blast.Searches
             return searchEntity;
         }
 
-        private void SubmitBatchJob(SearchEntity searchEntity, List<ResourceFile> resourceFiles)
+        private void SubmitBatchJob(SearchEntity searchEntity, IEnumerable<SearchQueryEntity> queries, List<ResourceFile> resourceFiles)
         {
             PoolInformation poolInfo;
 
@@ -188,32 +200,29 @@ namespace Microsoft.Azure.Batch.Blast.Searches
                 resourceFiles);
             job.Commit();
 
-            var tasks = GetTasks(searchEntity);
+            var tasks = GetTasks(searchEntity, queries);
             job.Refresh();
             job.AddTask(tasks);
 
-            job.Refresh();
-            job.OnAllTasksComplete = OnAllTasksComplete.TerminateJob;
+//            job.Refresh();
+//            job.OnAllTasksComplete = OnAllTasksComplete.TerminateJob;
         }
 
-        public IEnumerable<CloudTask> GetTasks(SearchEntity searchEntity)
+        private IEnumerable<CloudTask> GetTasks(SearchEntity searchEntity, IEnumerable<SearchQueryEntity> queries)
         {
             var taskId = 0;
-            foreach (var filename in searchEntity.Files)
+            foreach (var query in queries)
             {
-                var outputFilename = GetQueryFilename(searchEntity.OutputfileFormat, taskId.ToString());
-                var blastOutputFilename = GetLogFilename(taskId.ToString());
-
                 var cmd = string.Format("/bin/bash -c '{0}; result=$?; {1}; exit $result'",
-                    GetBlastCommandLine(searchEntity.DatabaseId, searchEntity.Executable, searchEntity.ExecutableArgsSanitised, filename, outputFilename, blastOutputFilename),
+                    GetBlastCommandLine(searchEntity.DatabaseId, searchEntity.Executable, searchEntity.ExecutableArgsSanitised, query.QueryFilename, query.QueryOutputFilename, query.LogOutputFilename),
                     GetUploadCommandLine(searchEntity.OutputContainer));
 
                 var task = new CloudTask(taskId.ToString(), cmd);
-                task.DisplayName = filename;
+                task.DisplayName = query.QueryFilename;
                 task.UserIdentity = new UserIdentity(new AutoUserSpecification(elevationLevel: ElevationLevel.Admin));
                 task.ResourceFiles = new List<ResourceFile>
                 {
-                    new ResourceFile(_blobStorageProvider.GetBlobSAS(searchEntity.InputContainer, filename), filename)
+                    new ResourceFile(_blobStorageProvider.GetBlobSAS(searchEntity.InputContainer, query.QueryFilename), query.QueryFilename)
                 };
 
                 task.EnvironmentSettings = new[]
@@ -227,18 +236,27 @@ namespace Microsoft.Azure.Batch.Blast.Searches
             }
         }
 
-        private static string GetQueryFilename(string outputFilenameFormat, string taskId)
+        private static string GetQueryOutputFilename(string outputFilenameFormat, string taskId)
         {
+            // outputFilenameFormat is only used here to determine if we should use the old legacy names.
+            if (string.IsNullOrEmpty(outputFilenameFormat))
+            {
+                return string.Format("queryoutput-{0}.xml", taskId);
+            }
             return string.Format(outputFilenameFormat, taskId);
         }
 
-        private static string GetLogFilename(string taskId)
+        private static string GetLogFilename(string outputFilenameFormat, string taskId)
         {
+            if (string.IsNullOrEmpty(outputFilenameFormat))
+            {
+                return string.Format("blastoutput-{0}.log", taskId);
+            }
             return string.Format("log-{0}.txt", taskId);
         }
 
         private string GetBlastCommandLine(string databaseName, string executable, string executableArgs,
-            string queryFilename, string queryOutputFilename, string blastOutputFilename)
+            string queryFilename, string queryOutputFilename, string logOutputFilename)
         {
             var outputFormat = "-outfmt 5"; // XML
             if (!string.IsNullOrEmpty(executableArgs) && executableArgs.Contains(" -outfmt "))
@@ -254,7 +272,7 @@ namespace Microsoft.Azure.Batch.Blast.Searches
                 outputFormat,
                 queryOutputFilename,
                 executableArgs,
-                blastOutputFilename);
+                logOutputFilename);
         }
 
         /// <summary>
@@ -304,13 +322,12 @@ namespace Microsoft.Azure.Batch.Blast.Searches
         public JobManagerTask GetJobManagerTask(string searchId, List<ResourceFile> resourceFiles)
         {
             var cmd =
-                string.Format("/bin/bash -c 'python3 jobmanager.py {0} {1} {2} {3} {4} {5} {6} {7} {8}'",
+                string.Format("/bin/bash -c 'python3 SearchJobManager.py {0} {1} {2} {3} {4} {5} {6} {7}'",
                 _storageCredentials.Account,
                 _storageCredentials.Key,
                 _batchCredentials.Account,
                 _batchCredentials.Key,
                 _batchCredentials.Url,
-                typeof(SearchEntity).Name, // Table name
                 "$AZ_BATCH_JOB_ID",
                 SearchEntity.AllUsersPk, // PK for JobMananger
                 searchId); // RK for JobManager
@@ -322,7 +339,8 @@ namespace Microsoft.Azure.Batch.Blast.Searches
                 RunExclusive = false,
                 UserIdentity = new UserIdentity(new AutoUserSpecification(elevationLevel: ElevationLevel.Admin)),
                 ResourceFiles = resourceFiles,
-                Constraints = new TaskConstraints(null, null, 3),
+                Constraints = new TaskConstraints(null, null, 5),
+                KillJobOnCompletion = true,
             };
         }
 
@@ -430,7 +448,7 @@ namespace Microsoft.Azure.Batch.Blast.Searches
             return _tableStorageProvider.ListEntities<SearchEntity>(SearchEntity.AllUsersPk);
         }
 
-        public IEnumerable<SearchQuery> ListSearchQueries(Guid searchId)
+        public IEnumerable<SearchQueryEntity> ListSearchQueries(Guid searchId)
         {
             var entity = _tableStorageProvider.GetEntity<SearchEntity>(SearchEntity.AllUsersPk, searchId.ToString());
 
@@ -439,9 +457,24 @@ namespace Microsoft.Azure.Batch.Blast.Searches
                 throw new Exception("No such search " + searchId);
             }
 
+            if (entity.Version == 0)
+            {
+                return ListLegacySearchQueries(entity);
+            }
+
+            if (entity.Version == 1)
+            {
+                return ListV1SearchQueries(entity);
+            }
+
+            throw new ArgumentException("Unknown search version: " + entity.Version);
+        }
+
+        private IEnumerable<SearchQueryEntity> ListLegacySearchQueries(SearchEntity entity)
+        {
             IEnumerable<QueryOutput> queryOutputs = GetAllQueryOutputs(entity).ToList();
 
-            List<SearchQuery> searchQueries = new List<SearchQuery>();
+            List<SearchQueryEntity> searchQueries = new List<SearchQueryEntity>();
 
             try
             {
@@ -450,16 +483,16 @@ namespace Microsoft.Azure.Batch.Blast.Searches
 
                 foreach (var task in tasks)
                 {
-                    var queryOutput = GetQueryFilename(entity.OutputfileFormat, task.Id);
-                    var logOutput = GetLogFilename(task.Id);
+                    var queryOutput = GetQueryOutputFilename(entity.OutputfileFormat, task.Id);
+                    var logOutput = GetLogFilename(entity.OutputfileFormat, task.Id);
                     var outputs =
                         queryOutputs.Where(output => output.Filename == queryOutput || output.Filename == logOutput)
                             .ToList();
 
-                    searchQueries.Add(new SearchQuery
+                    searchQueries.Add(new SearchQueryEntity
                     {
                         Id = task.Id,
-                        InputFilename = task.DisplayName,
+                        QueryFilename = task.DisplayName,
                         Outputs = outputs,
                         State = BatchToQueryState(task),
                         StartTime = task.ExecutionInformation?.StartTime,
@@ -470,20 +503,20 @@ namespace Microsoft.Azure.Batch.Blast.Searches
             catch (Exception)
             {
                 var inputFiles = entity.Files;
-                foreach (var queryNumber in Enumerable.Range(0, (int) entity.TotalTasks))
+                foreach (var queryNumber in Enumerable.Range(0, (int)entity.TotalTasks))
                 {
-                    var queryOutput = GetQueryFilename(entity.OutputfileFormat, queryNumber.ToString());
-                    var logOutput = GetLogFilename(queryNumber.ToString());
+                    var queryOutput = GetQueryOutputFilename(entity.OutputfileFormat, queryNumber.ToString());
+                    var logOutput = GetLogFilename(entity.OutputfileFormat, queryNumber.ToString());
                     var outputs =
                         queryOutputs.Where(output => output.Filename == queryOutput || output.Filename == logOutput)
                             .ToList();
 
                     try
                     {
-                        searchQueries.Add(new SearchQuery
+                        searchQueries.Add(new SearchQueryEntity
                         {
                             Id = queryNumber.ToString(),
-                            InputFilename = inputFiles[queryNumber],
+                            QueryFilename = inputFiles[queryNumber],
                             Outputs = outputs,
                             State = QueryState.Success,
                             StartTime = null,
@@ -500,6 +533,25 @@ namespace Microsoft.Azure.Batch.Blast.Searches
             return searchQueries;
         }
 
+        private IEnumerable<SearchQueryEntity> ListV1SearchQueries(SearchEntity entity)
+        {
+            IEnumerable<QueryOutput> queryOutputs = GetAllQueryOutputs(entity).ToList();
+
+            var queries = _tableStorageProvider.ListEntities<SearchQueryEntity>(entity.Id.ToString()).ToList();
+
+            foreach (var searchQueryEntity in queries)
+            {
+                var queryOutput = GetQueryOutputFilename(entity.OutputfileFormat, searchQueryEntity.Id);
+                var logOutput = GetLogFilename(entity.OutputfileFormat, searchQueryEntity.Id);
+                var outputs =
+                    queryOutputs.Where(output => output.Filename == queryOutput || output.Filename == logOutput)
+                        .ToList();
+                searchQueryEntity.Outputs = outputs;
+            }
+
+            return queries;
+        }
+
         private QueryState BatchToQueryState(CloudTask task)
         {
             switch (task.State)
diff --git a/LifeSciences/AzureBlast/AzureBlast/Searches/ISearchProvider.cs b/LifeSciences/AzureBlast/AzureBlast/Searches/ISearchProvider.cs
index c24d070..3e05d17 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Searches/ISearchProvider.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Searches/ISearchProvider.cs
@@ -19,7 +19,7 @@ namespace Microsoft.Azure.Batch.Blast.Searches
 
         IEnumerable<SearchEntity> ListSearches();
 
-        IEnumerable<SearchQuery> ListSearchQueries(Guid searchId);
+        IEnumerable<SearchQueryEntity> ListSearchQueries(Guid searchId);
 
         string GetSearchQueryOutput(Guid searchId, string queryId, string filename);
     }
diff --git a/LifeSciences/AzureBlast/AzureBlast/Searches/SearchQuery.cs b/LifeSciences/AzureBlast/AzureBlast/Searches/SearchQuery.cs
deleted file mode 100644
index bfa051b..0000000
--- a/LifeSciences/AzureBlast/AzureBlast/Searches/SearchQuery.cs
+++ /dev/null
@@ -1,35 +0,0 @@
-// Copyright (c) Microsoft Corporation. All rights reserved.
-// Licensed under the MIT License. See License.txt in the project root for license information.
-
-using System;
-using System.Collections.Generic;
-
-namespace Microsoft.Azure.Batch.Blast.Searches
-{
-    public class SearchQuery
-    {
-        public string Id { get; set; }
-
-        public QueryState State { get; set; }
-
-        public DateTime? StartTime { get; set; }
-
-        public DateTime? EndTime { get; set; }
-
-        public string Duration
-        {
-            get
-            {
-                if (StartTime == null || EndTime == null)
-                {
-                    return "";
-                }
-                return (EndTime.Value - StartTime.Value).GetFriendlyDuration();
-            }
-        }
-
-        public string InputFilename { get; set; }
-
-        public IEnumerable<QueryOutput> Outputs { get; set; }
-    }
-}
diff --git a/LifeSciences/AzureBlast/AzureBlast/Searches/SearchSpecification.cs b/LifeSciences/AzureBlast/AzureBlast/Searches/SearchSpecification.cs
index a9096e9..4d61de5 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Searches/SearchSpecification.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Searches/SearchSpecification.cs
@@ -17,6 +17,10 @@ namespace Microsoft.Azure.Batch.Blast.Searches
 
         public IEnumerable<SearchInputFile> SearchInputFiles { get; set; }
 
+        public bool SplitSequenceFile { get; set; }
+
+        public int SequencesPerQuery { get; set; }
+
         public string PoolId { get; set; }
 
         public int? TargetDedicated { get; set; }
diff --git a/LifeSciences/AzureBlast/AzureBlast/Storage/AzureTableStorageProvider.cs b/LifeSciences/AzureBlast/AzureBlast/Storage/AzureTableStorageProvider.cs
index 15420ac..3cf0d80 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Storage/AzureTableStorageProvider.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Storage/AzureTableStorageProvider.cs
@@ -27,6 +27,18 @@ namespace Microsoft.Azure.Batch.Blast.Storage
             table.Execute(insertOperation);
         }
 
+        public void InsertEntities<T>(IEnumerable<T> entities) where T : TableEntity
+        {
+            CloudTable table = _cloudTableClient.GetTableReference(typeof(T).Name);
+            table.CreateIfNotExists();
+            TableBatchOperation batchInsert = new TableBatchOperation();
+            foreach (var entity in entities)
+            {
+                batchInsert.Insert(entity);
+            }
+            table.ExecuteBatch(batchInsert);
+        }
+
         public void UpdateEntity<T>(T entity) where T : TableEntity
         {
             CloudTable table = _cloudTableClient.GetTableReference(entity.GetType().Name);
diff --git a/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchEntity.cs b/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchEntity.cs
index 7956782..24c04cd 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchEntity.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchEntity.cs
@@ -23,6 +23,7 @@ namespace Microsoft.Azure.Batch.Blast.Storage.Entities
         {
             PartitionKey = AllUsersPk;
             RowKey = queryId.ToString();
+            Version = 1;
         }
 
         public Guid Id { get { return Guid.Parse(RowKey); } }
@@ -33,6 +34,8 @@ namespace Microsoft.Azure.Batch.Blast.Storage.Entities
 
         public Int64 CompletedTasks { get; set; }
 
+        public int Version { get; set; }
+
         public string InputContainer { get; set; }
 
         public string OutputContainer { get; set; }
diff --git a/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchQueryEntity.cs b/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchQueryEntity.cs
new file mode 100644
index 0000000..755159d
--- /dev/null
+++ b/LifeSciences/AzureBlast/AzureBlast/Storage/Entities/SearchQueryEntity.cs
@@ -0,0 +1,64 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Microsoft.Azure.Batch.Blast.Searches;
+using Microsoft.WindowsAzure.Storage.Table;
+
+namespace Microsoft.Azure.Batch.Blast.Storage.Entities
+{
+    public class SearchQueryEntity : TableEntity
+    {
+        public SearchQueryEntity(Guid searchId, string queryId)
+        {
+            PartitionKey = searchId.ToString();
+            RowKey = queryId;
+            CreationTime = DateTime.UtcNow;
+        }
+
+        public SearchQueryEntity()
+        { }
+
+        public string Id { get { return RowKey; } set { RowKey = value; } }
+
+        public string OutputContainer { get; set; }
+
+        public string QueryFilename { get; set; }
+
+        public string LogOutputFilename { get; set; }
+
+        public string QueryOutputFilename { get; set; }
+
+        public string _State { get; set; }
+
+        [IgnoreProperty]
+        public QueryState State
+        {
+            get { return (QueryState)Enum.Parse(typeof(QueryState), _State); }
+            set { _State = value.ToString(); }
+        }
+
+        public DateTime CreationTime { get; set; }
+
+        public DateTime? StartTime { get; set; }
+
+        public DateTime? EndTime { get; set; }
+
+        [IgnoreProperty]
+        public string Duration
+        {
+            get
+            {
+                if (StartTime == null || EndTime == null)
+                {
+                    return "";
+                }
+                return (EndTime.Value - StartTime.Value).GetFriendlyDuration();
+            }
+        }
+
+        [IgnoreProperty]
+        public IEnumerable<QueryOutput> Outputs { get; set; }
+    }
+}
diff --git a/LifeSciences/AzureBlast/AzureBlast/Storage/ITableStorageProvider.cs b/LifeSciences/AzureBlast/AzureBlast/Storage/ITableStorageProvider.cs
index e955f9f..73eae56 100644
--- a/LifeSciences/AzureBlast/AzureBlast/Storage/ITableStorageProvider.cs
+++ b/LifeSciences/AzureBlast/AzureBlast/Storage/ITableStorageProvider.cs
@@ -10,6 +10,8 @@ namespace Microsoft.Azure.Batch.Blast.Storage
     {
         void InsertEntity<T>(T entity) where T : TableEntity;
 
+        void InsertEntities<T>(IEnumerable<T> entities) where T : TableEntity;
+
         void UpdateEntity<T>(T entity) where T : TableEntity;
 
         void UpsertEntity<T>(T entity) where T : TableEntity;