Psiblast 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 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 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 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 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 ArticleAnalyzing Overlap Of Results Between Blast Queries. Is There A Tool For This?...
I am using various set of enzymes organized into classes in my research. As part of this I use PSI-BLAST to increase the size of my data sets. I known there is a large amount of overlap returned in the...
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 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 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 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 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 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 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 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 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 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 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 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 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...
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