Extract Unmapped Reads From Blast
Is there a way to tell blast to output the unmapped reads into a separate file or at least the name of the unmapped sequences?
View ArticleRecovering Positions Of Identical Matches From Multiple/ Pairwise Sequence...
I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a...
View ArticleProblem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
View ArticleWhat Exactly Does Formatdb Do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
View ArticleNCBI blast PHP API choice
Hello.I want to program a web application, based on PHP language. One of its features, will be the ability to send data and receive results to/from ncbi's server and then analyze them with other...
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 ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
View ArticleAbout Blast Scores In Matrix Format.
Hi All, How Can I get local Blast score in matrix format??( I have score but I need in Matrix format) How can I run blast of 200 sequences in order to alignment sequences by writing a python...
View ArticleBlast 2.2.24+ Database Error
When running local BLAST on a big database (all human proteins) I get the following error:proteinsApplicationError: Command 'blast-2.2.24+/bin/blastp.exe -query "query.fasta" - db...
View Articlegetting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleHow to perform BLAST search containing a large number of query sequences ?
I need to BLAST a large number of query sequences in one go. How might I go about this ? I have a .rtf file containing a large number of query sequences ... in this...
View ArticleHow To Concatenate/Merge Blast Xml Outputs?
I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates...
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 ArticleRunning Blast With C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
View ArticleBlast Settings For Short Sequences
I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:>ponzr CGCGGTAAAACACATTTG And...
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleTrinity/Rsem/Edger Pipeline...Now What?
HI people,I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...I basically have 3 sample condtions -with 3 replicates...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
View Article