[BiO BB] how to visit NCBI Blast and get the plain text resultusing script

Mike Marchywka marchywka at hotmail.com
Wed Mar 21 11:45:09 EDT 2007


ftp://ftp.ncbi.nih.gov/blast/documents/

As for the earlier issue,you can compare executing a binary:

echo -e ">${NAME}\n${SEQ}\n"  | blastcl3 ${BL} > .temp_blastnew_1

To trying to work around the web interface::

QS1="QUERY=${SEQ}"
QS2="&QUERY_FROM=&QUERY_TO=&DATABASE=nr&ENTREZ_QUERY=&ENTREZ_QUERY=All+organisms&COMPOSITION_BASED_STATISTICS=0"
QS3="&EXPECT=${expect}&WORD_SIZE=2&MATRIX_NAME=PAM30&GAPCOSTS=9+1&PSSM=&OTHER_ADVANCED=&PHI_PATTERN=&SHOW_OVERVIEW=on"
QS4="&SHOW_LINKOUT=on&GET_SEQUENCE=on&NCBI_GI=on&FORMAT_OBJECT=Alignment&FORMAT_TYPE=${format}&MASK_CHAR=0&MASK_COLOR=0"
QS5="&DESCRIPTIONS=1000&ALIGNMENTS=1000&ALIGNMENT_VIEW=Pairwise&I_THRESH=0.005&FORMAT_ENTREZ_QUERY="
QS6="&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH=&LAYOUT=TwoWindows&FORMAT_BLOCK_ON_RESPAGE=None"
QS7="&AUTO_FORMAT=Semiauto&PROGRAM=blastp&CLIENT=web&SERVICE=plain&PAGE=Proteins&CMD=Put"

QUERYSTR="${QS1}${QS2}${QS3}${QS4}${QS5}${QS6}${QS7}"

POSTURL="http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi"
LYNXCMD="lynx -width=0 -source -accept_all_cookies -dump -post_data "
echo $QUERYSTR | lynx -width=0 -source -accept_all_cookies -dump -post_data 
"${POSTURL}" > .temp_blast_0







>From: David <dgw106 at york.ac.uk>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] how to visit NCBI Blast and get the plain text 
>resultusing script
>Date: 21 Mar 2007 14:13:21 +0000
>
>Dear Lily,
>
>You can download and run BLAST locally to save network traffic, if you 
>prefer, especially if you have many queries to run. Binaries are available 
>for many platforms at http://www.ncbi.nlm.nih.gov/BLAST/. Of course, you 
>need space to store the databases. For example, the non-redundant protein 
>sequence database is a few hundred MB I think...
>
>Parsing BLAST XML output (using the option '-m 7' when running BLAST from 
>the command line) can be done easily using the NCBIXML module in Biopython.
>
>This method has the feature that you have a static BLAST version and 
>database, so allows for reproducibility, which can be viewed as an 
>advantage or disadvantage, depending what you want to do.
>
>Cheers
>David

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