How to do automated blast with mulitple sequences and BLAST each one...
Is there an automated program that can take mulitple sequences and BLAST each one individually???
View ArticleIncomplete Blast Database In Ubuntu
hello all, i am trying to do local blast using this command blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.outi am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded...
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 ArticleMegablast, Makembindex, And Choosing Nmers
I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18. It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when...
View ArticleCan Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline...
Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by putting the stdout from the wrapper into a python string variable and then using NCBIXML.parse to parse...
View ArticleAnnotating sequences after de-novo Trinity assembly and RSEM analysis...there...
Hello, I'm hoping someone can provide some insight or point me in the right direction... I have very little programming knowledge and am fairly new to RNA-seq but I'm sure there must be an easier way...
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 ArticleBiopython Local Blast Not Producing File
Hello, I am a Computer Science & Molecular Biology Student at MIT. I am currently working on my research project in the Research Laboratory of Electronics and I am trying to solve a problem while...
View ArticleWhy When I Use Blastdbcmd With The Fasta Database It Doesn'T Recognize The...
nr database is presented in two version. One is the FASTA and there is another one.
View ArticleAlign Paired End Reads Using Blast
Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...
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 ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
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 ArticleUsing Ncbi-Blast-2.2.25+ Remote Flag. Where Can I Find The List Of Databases...
Hello.I am trying to blast using -remote flag to use the databases on the remote server. The problem is I don't know the name of the datbases for the -db flag. Is there any website where I can get the...
View ArticleIndividual Hit Gene Information From Qblast Xml Output
I've just started using Biopython, and I am trying to perform remote BLAST operations using the qblast() function. Everything seems to be working properly, but I am not being able to retrieve an...
View ArticleTo locate some introgressed QTL regions of an assembly?
I need to locate some introgressed QTL regions of an assembly (resulted from backcrossing) to analyze those regions further. I have SSR marker sequences (associated with those QTL regions) as well....
View Articlerps blast database 'formatrpsdb' problem
Hi.. After installing BLAST+ package from ncbi, when i try to build a database for rps blast analysis using: formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0 it gives following error:...
View ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
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...
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