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 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 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 ArticlePerl Script For Blast+
Hi, how can I blast using perl script as I have whole database i.e subject with me and a single protein file is arranged in FASTA format. I have used Blast+ for the creation of database and have three...
View ArticleSetting Up Blast Server
Hi, i'm trying to set up my own blast server for convenience and i'm having some technical issues which might not be purely bioinformatics related but i hope someone here has done it before.My problem...
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 ArticleWhere Should I Start From ?
Hi all . I'm new to this field as I'm working on my thesis , and I'm kind of lost here .My main objective is to prove the hypothesis assumes that Microsatellites regions in plants genomes could be one...
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 ArticleGetting Taxonomic Blast Table Output Of 2.2.28 Using A Local Copy Of Nt
Hello!I understand that taxonomic information for each blast HSP can now be output in the blast custom table format new in blast+ 2.2.28. My simple question is: how do I set up a local copy of NCBI's...
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 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 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 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 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 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 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 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 ArticleRunning Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
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