Blast+: 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 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 ArticleHow Can I Record A Specific Domain Sequence Within A Protein Query?
Hello everyone: I'm just beginning with massive search on my own database of proteins and I need some guidelines to start. What I'm trying to do is recording (as *.fasta file) a specific domain...
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 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 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 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 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 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 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 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 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 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 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 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 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...
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