Fastest 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 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 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 Articleblast -F F equivalent in blast+
In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false)In blast+ I couldn't figure out the...
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 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 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 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 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 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 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 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 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 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 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+ 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 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 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 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...
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