How 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 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 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 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 ArticleFastest Way To Search For Perfect Matches Only In Blast Or Blat
Hi, I have a numerous 100-mer sequences (let's say billions). What I am going to do is to query these sequences to entire human genome to find "perfect matches" only.I first tried to do this using...
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 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 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 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 ArticleA Tool For Flagging Blast Searches?
I want to know if there is a blast way or a blast-like tool in which a query will search through a database and return only predetermined hits based on given flags like sequence fasta ids. To be more...
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 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...
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 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 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 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 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 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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