NCBI 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 ArticleLegacy Blastx output (Karlin-Altschul statistics) from XML output
If have to generate legacy blastx output from Blast XML output (why do people still require this!!!?). The legacy output has a block starting with Score E Sequences producing significant alignments:...
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 ArticleMultiple PSI-BLAST iterations from command line using remote database
When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working...
View ArticleHow to get BLAST+ (stand alone blast) output to contain only the first hit...
Greetings! I'm using BLAST+ v. 2.2.26, and would like to customize the output to include only the FIRST hit for each separate record in the data base. The region I am using as the query is a domain...
View ArticleParsing Blast results for different genus
Dear All,I have obtained several .gb BLAST results that I want to split in different .gb or .fasta files accordingly to genus.I searched for different ways to do it in the web, but didn't find a way to...
View ArticleHow to BLAST a fasta file that is non-16S
Hello,I have a Illumnia generated fasta file that was created using rpoB sequence data. I am looking to BLAST these sequences in order to find the best 3 hits of what organism I am looking at. I know...
View ArticleRetrieving results using BLAST SOAP API
Hi ;I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:"blasp.exe -query input.txt -db pdbaa...
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 Articleorthomcl blast error: no hits are being saved
when i try to run blast in orthomcl using the command below:blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes -soft_masking true...
View ArticleHow to use the RECON package to identify repeat families from genomic sequences
I'm trying to learn RECON and am experimenting using chr22. My steps so far, roughly:Make blast database from chr22.faBLAST chr22.fa against its own databaseRun MSPCollect.pl (RECON provided script) to...
View Articlecorrelate gi identifiers with GO identifiers
Hi there,I am looking for a tool that correlates a list of GI identifiers with known GO identifers.
View Article"penicillin-binding protein dimerization domain / penicillin-binding protein,...
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View Articlehow to blast multiple contigs to the reference database?
i have multiple contigs in fasta format after assembling the reads. i also have 33 reference genome sequences. i want to blast the query sample sequence to my reference sequences as well as the plasmID...
View ArticleWhat is the algorithm behind the sequence comparison in Uniprot or in any...
Hi, This is Shrujan, i wnat to know the algorithm behind the Sequence comparison in Uniprot or in any other database, which does BLAST. I need your valuable suggestions and guidance.Thanks &...
View ArticleTrying to extract BLAST results into xml outfile from larger BLAST xml file
This is probably a fairly basic question, so I apologize in advance, but I can't seem to figure out how to output xml format using Biopython. Basically, I have a fairly large BLAST results file in xml...
View ArticleHow to get the result which mismatch 1 to the query sequence by...
the program is blastn -task blastn-short -query rfam_trimed_short_uniq.fa -db /root/bio-analysis-soft/database/gss-est-db/tage -ungapped -penalty -1 -reward 1 -outfmt 6 -out 2 -num_threads 12I get an...
View ArticleBLAST E value calculation
I'm trying to work out the formula for BLAST e value calculation. I have surfed all across the internet looking for it, but the only thing I'm able to find is the formula provided here:...
View ArticleBlast multifasta against NCBI nr database, and download all the results
Hello, i have a fasta file with 7600 nucleotide sequences, i have a local nr database formated for blast, with makeblastdb, i don't use formatdb because it give errors (zero length sequences). I blast...
View ArticleExact matching with bowtie, BLAT and BLAST+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, e.g.: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa >...
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