Blast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleOnline Blast Perl/Python Script
Hi AllI have a 10000 sequences in fasta file which I want to do online blast with nr data base . Do any one of you has any perl or python script to do that?Thanks in advanceRegards
View ArticleHow do I blast against a specific portion of the nr database?
I would like to blast my sequences against the swissprot database, using local blast. For the purpose of downstream applications, I would like to do this using the copy of the swissprot database from...
View ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
View ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
View ArticleBlastdbcmd - Too Many Positional Arguments , The Offending Value: %F - Windows
Hey guys, I'm trying to use blastdbcmd - when I type the following on cmdblastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txtthe following error pops up:Error: Too many positional...
View ArticleHelp! I Can Successfully Run A Blastp Search In Bioperl But I Want To Also...
I am new to Perl/Bioperl and have run into a problem. How can I perform a blastn search on a DNA sequence? I can successfully perform a BLASTP search, but I can't find any documentation in cpan or...
View ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleIs Matching Blastn Output A Requirement For Alternative Sequence Matching...
I've read a paper demonstrating an implementation of sequence alignment and the authors indicate that in order to provide substantial speed gains they must compromise on query size and output fidelity,...
View ArticleBest Hits From Blast Tabular Output Of Multiple-Queries
Hello. I have been trying to get the best hits out of blast output files. I know that -v option or maxtargetseqs in standalone blast gives the best ones. But I already have a huge output of multiple...
View ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View Articleblastn cannot find the database
I'm new to BLAST and am trying to run a legacy blast command using blast+. I have downloaded the human_genome databases and unzipped and untarred them.The databases are in:...
View ArticleMapping blast xml report elements to their variable names in biopython
Hi all ^_^ Im working on a script in biopython that extracts SSR's from some plant species , blast their sequences against each other and group the results of similarity based on some coverage value ....
View ArticleGet Blast Database Size
I have piped unknown length sequences into makeblastdb. Now I want to know total length of those sequences (BLAST database size).Example: # "cat" is used as an example # My "real" sequences are piped...
View Articlelocal tblastx error
Hi, I am getting following error while running tblastx against NR database “BLAST Database error: No alias or index file found for nucleotide database [/data/ncbi/blastdb/nr]My seq is nucleotide, Blast...
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleWhat Program Or Database To Use To Analyze Blast Result Output?
Hello, I ran the blast locally and got the blast output like followingquery1 gi|4003386|dbj|AB020866.1| 98.44 64 1 .. query2 gi|60834728|gb|AY894071.1| 92.11 76 2 ... query3 gi|21618453|gb|BC032801.1|...
View Articleerror downloading refseq for local BLAST install via FTP
I am having trouble downloading the refseq database required for BLAST+. I am following the instructions from http://www.ncbi.nlm.nih.gov/books/NBK52640/ but get No such file or Directory error using...
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