Blast 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 ArticleBlast+ Nucleotide "-Matrix" Command
HI, I've been trying to run a nucleotide blast (blastn) using BLAST+ here is what it should look like using legacy blast: blastall -p blastn -d db -i fasta.fasta -o output.blastn -e 10000 -F F -a 7 -M...
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 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 ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
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 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 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 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 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 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 ArticleIs It Possible To Use Blast+ To Hit Embl Database?
I am having nightmare in using NCBI-BLAST+ for last two weeks. Now blasting remote database became very slow irrespective of my computer or my internet connectivity speed. I am thinking to use EMBL-EST...
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 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 ArticleBlastclust Has Been Depreciated. Does Anyone Know Why?
I am working on machine learning project using SVMs. One of the steps in the preparation of my data sets is to reduce the sequence similarity in each class to 40%. I have compared CD-HIT and BLASTCLUST...
View ArticleBlastdb_Aliastool Error
Hi everyone,I would like to build a human+bacteria+archaea subset of the nr database. So what I did is:Get the nr databaseGet the GI list of human+bacteria+archaea from Entrez Protein databaseUse this...
View ArticleBlast+ Nucleotide "-Matrix" Command
HI, I've been trying to run a nucleotide blast (blastn) using BLAST+ here is what it should look like using legacy blast: blastall -p blastn -d db -i fasta.fasta -o output.blastn -e 10000 -F F -a 7 -M...
View ArticleAbout Percent_Identity And Bio::Searchio
Hi, I have a question regards of how Bio::SearchIO calculate the percent identity in an alignment. I have this tabular output (called blasttest2 and its just a minimal fraction of a very large 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 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...
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