BLAST - Revision history

Smith: /* Technical Notes */

2015-01-27T04:41:56Z

‎Technical Notes

2015-01-27T04:37:23Z

‎References

2015-01-27T04:36:19Z

‎At the bottom of the pane

2015-01-27T04:29:38Z

‎At the bottom of the pane

2015-01-27T04:18:29Z

‎Technical Notes

2015-01-27T04:07:39Z

‎Technical Notes

2015-01-27T04:06:26Z

‎Technical Notes

2015-01-27T04:05:44Z

‎Technical Notes

2015-01-27T03:13:31Z

‎Analysis Controls - releases 2.2.2 and earlier

2015-01-27T02:56:32Z

‎For proteins:

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 * When geWorkbench is asked to submit multiple sequences to the NCBI BLAST server, it will submit them one at a time and wait for the results before submitting the next sequence.  This is done to simplify the subsequent parsing and display of the results.
 * '''Metagenome databases''' - The Whole Genome Shotgun (WGS) databases at NCBI include the metagenome samples. The metagenomic, or "environmental" samples sequences are currently also available in the env_nt and env_nr (metagenomic) databases, but this may not always be true.  The NCBI BLAST website now only supports searching metagenomic projects through the WGS database. However, geWorkbench does not directly support searching the metagenomic projects via the WGS database, and instead continues to provide direct query of the metagenomes via env_nt and env_nr. (Additional details in Mantis #3198, #3801).
 =References=

← Older revision		Revision as of 04:37, 27 January 2015
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	* Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. (2000) Winnowing sequences from a database search. J Comput Biol. 7(1-2):293-302.		* Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. (2000) Winnowing sequences from a database search. J Comput Biol. 7(1-2):293-302.

−	* The ~~NCIB~~ BLAST site provides a comprehensive [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=References list of references].	+	* The NCBI BLAST site provides a comprehensive [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=References list of references].

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 * '''Reset''' - uncheck all "Include" boxes.
 * '''Select All''' - mark as checked all the "Include" boxes.
-* '''Add Selected Sequences to Workspace''' - for each hit whose "Include" box is checked, add its full sequence to a sequence node in the [[Workspace|Workspace]].  This option performs a retrieval query against the NCBI database to fetch the full sequence corresponding to each selected hit, not just the aligned portions.
+* '''Add Complete Sequences to Workspace''' - for each hit whose "Include" box is checked, add its full sequence to a sequence node in the [[Workspace|Workspace]].  This option performs a retrieval query against the NCBI database to fetch the full sequence corresponding to each selected hit, not just the aligned portions.
 ** Technical note - The query uses the integer Entrez database id (e.g. GI number) for a sequence, and this id will be reflected in the fasta format sequence entry returned as a sequence node to the Workspace.
 * '''Only Add Aligned Parts''' - for each hit whose "Include" box is checked, add to the [[Workspace|Workspace]] only the portion(s) of its sequence which aligned with the query sequence.  The new sequence node will contain one sequence for each aligned region.

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 * '''Add Selected Sequences to Workspace''' - for each hit whose "Include" box is checked, add its full sequence to a sequence node in the [[Workspace|Workspace]].  This option performs a retrieval query against the NCBI database to fetch the full sequence corresponding to each selected hit, not just the aligned portions.
 ** Technical note - The query uses the integer Entrez database id (e.g. GI number) for a sequence, and this id will be reflected in the fasta format sequence entry returned as a sequence node to the Workspace.
-* '''Only Add Aligned Parts''' - for each hit whose "Include" box is checked, add to the [[Workspace|Workspace]] only the portion of its sequence which aligned with the query sequence.  The new sequence node will only contain the sequence shown in the alignment on the Subject line(s) (with gaps removed).
+* '''Only Add Aligned Parts''' - for each hit whose "Include" box is checked, add to the [[Workspace|Workspace]] only the portion(s) of its sequence which aligned with the query sequence.  The new sequence node will contain one sequence for each aligned region.
 ** Technical note - these sequences will be displayed with the accession number, as was the original hit.
 *** The tag "---PARTIALLY INCLUDED" will also be appended to the accession number in the sequence node.

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 * The NCBI BLAST server may occasionally return an error when sequences are searched from geWorkbench. The problem appears to depend on the load on the NCBI BLAST server.
 * When geWorkbench is asked to submit multiple sequences to the NCBI BLAST server, it will submit them one at a time and wait for the results before submitting the next sequence.  This is done to simplify the subsequent parsing and display of the results.
-* '''Metagenome databases''' - The NCBI BLAST interface no longer directly lists the metagenomic databases, instead, individual metagenomic projects can be searched as part of the WGS search.  However, geWorkbench does not support this mechanism. geWorkbench still provides direct query of the metagenomes. (Additional details in Mantis #3198).
+* '''Metagenome databases''' - The Whole Genome Shotgun (WGS) databases at NCBI include the metagenome samples. The metagenomic, or "environmental" samples sequences are currently also available in the env_nt and env_nr (metagenomic) databases, but this may not always be true.  The NCBI BLAST website now only supports searching metagenomic projects through the WGS database. However, geWorkbench does not directly support searching the metagenomic projects via the WGS database, and instead continues to provide direct query of the metagenomes via env_nt and env_nr. (Additional details in Mantis #3198, #3801).
 =References=

← Older revision		Revision as of 03:13, 27 January 2015
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	[[Image:BLAST_Analysis_Progress_Dialog.png]]		[[Image:BLAST_Analysis_Progress_Dialog.png]]
−
−	~~==Analysis Controls - releases 2.2.2 and earlier==~~
−
−	* '''All Markers''' - if selected, use all sequences loaded, overriding any activated sets in the Marker Sets component.
−	* '''Total Sequence Number''' - indicates how many sequences have been selected for query.
−	* '''Curling arrow''' - start BLAST search
−	* '''Stop sign''' - stop BLAST search (if pushed, geWorkbench will not wait for or retrieve the BLAST results).
−
−	~~[[Image:T_SequenceAlignment_BLAST_general_controls.png]]~~

	=BLAST Results Viewer=		=BLAST Results Viewer=

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 * '''Non-redundant protein sequences (nr)'''
 * '''Reference proteins (refseq_protein)'''
-* '''Swissprot protein sequences (swissprot)'''
+* '''UniProtKB/Swiss-prot (swissprot)'''
 * '''Patented protein sequences (pat)'''
 * '''Protein Data Bank sequences (pdb)'''
-* '''Environmental samples (env_nr)'''
+* '''Metagenomic proteins (env_nr)'''
 ===Search Choice===