In Blast+, How Can I Ignore The *** No Hits Found *** In Output
Hi,Doing a blast+, using the default output ( -outfmt 0 ), there is a way to not save all the queries that doesn't hit ? I want to eliminate from output the lines around No hits found , I think it's...
View ArticleBioperl Standaloneblastplus, Cleaning Up Thousands Of Temp Files
Hi, I'm using StandAloneBlastPlus BioPerl module as NCBI blast+ wrapper. I have to perform sequence alignments against a database of bacteria using multiple processes on a cluster. A temp file (.fas)...
View ArticleCan Igv View Blast+ Output File?
Hi, I aligned short reads using blast+ and generated tabular file. I also have bam files generated by aligners, and I can visualize the bam file using IGV, my question is can I view the blast output...
View ArticleRun Makeblastdb For Compressed File
Hi all, Does anyone know how to make database for compressed file fasta.gz using blast? I am using the blast2.2.29+. I saw the tutorial of makeblastdb, there is no option for dealing with the fasta.gz...
View ArticleTrying To Run Psipred But Failing To Use Blastpgp
Hi - I am trying to run psipred (http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/) and it requires blast+ to be installed. I have done this, and all the blast executables are stored in...
View ArticleBiopython-Blast:Querying A Single Sequence Without Input File
Hello, I am studying the application of blast in biopython. Now a problem is troubling me. I have to create a fasta file to use the function NcbiblastpCommandline( which is similar to blastp in...
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...
View ArticleScientific Names In Blast Output And Databases
Hi, I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option -outfmt which can take sscinames(seems new in version Blast+ 2.2.28), but even...
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...
View ArticleHow To Blast Hundreds Of Fasta Files Using Local Database And Perl
I have to blast a zip file including hundreds of protein fasta files. Since it is impossible to blast them one by one, I plan to use perl to blast in a local database. I am new to perl and look for...
View ArticleWhy Do I Get A Makeblastdb Error: File Does Not Match Input Format Type,...
hello guys after giving the following command i am facing error for the output file being generated....However formatdb was able to accept my FASTA file and i was successfully able to run my blastn on...
View ArticleBlast On A Custom Galaxy Server Is Unable To Find Database
Hello,I am currently trying to use megablast on a Galaxy server. I use a custom db that I prepared with makeblastdb -in some_sequences.fasta -dbtype nucl -out some_sequences. I put the path to my...
View ArticleAnalyzing Overlap Of Results Between Blast Queries. Is There A Tool For This?...
I am using various set of enzymes organized into classes in my research. As part of this I use PSI-BLAST to increase the size of my data sets. I known there is a large amount of overlap returned in the...
View Article[Ncbi-Blast-2.2.28+] Thrownullpointerexception() When Running Blastn
Hello, I'm still rather new to blast+ and I'm trying to get an implemented tool to work locally(that already works somewhere else). The tool just completely skips blasting and doesn't even show me any...
View ArticleBioperl Standaloneblastplus, Cleaning Up Thousands Of Temp Files
Hi, I'm using StandAloneBlastPlus BioPerl module as NCBI blast+ wrapper. I have to perform sequence alignments against a database of bacteria using multiple processes on a cluster. A temp file (.fas)...
View ArticleHow To Get Fasta Source File From Blast Csv Format?
I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.Liketblastn -db dmel_a -query somequery.faa -outfmt 10The...
View ArticleHow To Stores The Query And Frequency Count Ratio Matrix In A File In Blast+
The command to generate a he query and frequency count ratio matrix using nr might look as follows: blastpgp -i test1.fa -d nr -h 0.0001 -j 4 -C $id$chain.nr.chk -Q test1.matrix -a2I need the...
View Articleblast -F F equivalent in blast+
In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false)In blast+ I couldn't figure out the...
View ArticleBlast+
Hi, I would want to know if Blast+ program (Windows version) converts Blast database format in FASTA format? Is the blastdbcmd executable right to do it? And how I must write the orden for do it? I...
View ArticleTruly Parallel Blasts With Blast+
Hi, I find myself once again having to run blast+ programs to blast large amounts of sequences (100,000+) on swissprot, refseq, nr, etc. blast+ can use multiple cores, but the way it is implemented...
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