How To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
View ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
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 ArticleHow can I convert the blast results into a matrix?
I've a table of blast results with ~5hits/query protein: ProteinClassProtA1ProtA1ProtA1ProtA0ProtA1ProtB1ProtB1ProtB0ProtB0ProtB1I would like to convert this into a feature vector matrix like this:...
View ArticleMpiblast Vs Blast+
How up-to-date is mpiBlast compared to blast+ from ncbi? I am not sure what the relation ship between mpiblast and blast+ is, is mpiBlast derived from blast+. blast+ seems to be multi-threaded, but I...
View ArticleBLAST: How much of the query is aligned?
At first, I thought this question would answered by the "qcovs" field, but a glance at the results proved that that isn't the case. To begin with, each qcovs value relates not to the original query,...
View ArticleHow To Use To Use Standalone Blast In Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short...
View ArticleBlast2Go Doesn'T Work With My Fasta File
Hi all, i downloaded human unigene fasta file from Here (Hs.seq.uniq.gz with .uniqe format), and change it to .fasta by notepad. when i submitted the file to blast2go it doesn't work and give me an...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleScript To Submit And Manage Blast Jobs On A Cluster?
Hi,I make use of a local cluster (managed through LSF) to BLAST large sequence sets. I wrote a basic script to split a fasta file and submit each part as a different BLAST job. Does anyone know of such...
View ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View Articlewhich factors help to select positive blastx result?
hello guys! i have BLASTXed a query file (which contain more than 140000 nucleotide sequences) with a db file (which contain more than 1400 polypeptide sequences). got the blasted query sequences...
View ArticleIs There An Explaination For Each Of The Pieces Of Blast Output?
I was wondering if there was full explanation for each of the pieces of this part of the output. Lambda K H 0.328 0.141 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties:...
View ArticleBlast more thn several DNA sequences
Can we blast several DNA sequences against whole genome simultaneously? If yes, thn How?
View ArticleForum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
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