From ae93a2dab938bd28f7887349b47e642ac765e48b Mon Sep 17 00:00:00 2001 From: Marco Del Tufo <marco.deltufo@exact-lab.it> Date: Tue, 4 Jul 2023 13:49:28 +0000 Subject: [PATCH] Update search-domain-services.md --- .../search-domain-services.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md index d2903f5fd2f..592ce4d226d 100644 --- a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md +++ b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md @@ -92,7 +92,15 @@ and used as command line parameters of the BLAST+ tools: |---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| |evalue |Defines the threshold of so-called "Expect Value" of found matches (for details see http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect and http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf). Higher values means more found matches. Default value is 10. | |word_size|Word size for initial match. Decreasing word size results in increasing number of matches. Default values (if task parameter hasn't been specified): 11 for blastn and 3 for blastp. | -|task |Defines values for a set of parameters of the tools blastn and blastp. Possible values are <ul><li>blastn: Default value blastn</li></ul> <ul><li>blastp: Default value blastp</li></ul> +|task |Defines values for a set of parameters of the tools blastn and blastp. Possible values are <ul><li>blastn: Default value blastn</li></ul>|Value |Description |Default value of word_size| +|------------|---------------------------------------------------------------------------------------------------------|--------------------------| +|blastn-short|blastn program optimized for sequences shorter than 50 bases |7 | +|blastn |Traditional blastn requiring an exact match of 11 |11 | +|dc-megablast|Discontiguous megablast used to find more distant (e.g., interspecies) sequences |11 | +|megablast |Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences|28 |<ul><li>blastp: Default value blastp</li></ul>|Value |Description |Default value of word_size| +|------------|-------------------------------------------------------------------|--------------------------| +|blastp |Traditional blastp to compare a protein query to a protein database|3 | +|blastp-short|blastp optimized for queries shorter than 30 residues |2 | |ungapped |If specified (with an empty string value) only ungapped matches are returned. Will be ignored for blastp. | -- GitLab