Ncbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
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 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 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...
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 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 ArticleIn 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 ArticleTrouble With Local Psiblast
Hello everyone,My requirement is to generate a PSSM (Position Specific Scoring Matrix) from a given protein fasta sequence against a protein database. I have downloaded and installed the latest version...
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 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 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 ArticleBlastp Of Human Proteins Against A Combined Pig And Gorilla Protein Db, Why...
wget ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/protein/protein.fa.gz wget ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/protein/protein.fa.gz wget...
View ArticleBlast+: Error Messege
I want to convert 16S Microbial pre-formatted database in fasta format. I use Blast+ program (2.2.27+ version Window). I could install this program and I know that I must to use blastdbcmd command. The...
View ArticlePsiblast Fasta Formatted Output
Hi,I have a FASTA formatted protein sequence (stored in DsbA.fa) and I would like to use PSI-BLAST (not the web server. The command line in the BLAST+ package) to generate hits. I am using the...
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 ArticleBlastn / Tblastn : Mapping The Features Of The Query To The Hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
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 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 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...
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