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 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 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 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+ 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 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 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 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 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 ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View ArticleAveraging Blast Results
I'm in a situation where I have two sets of BLAST results, and I'd like to compare them (non-rigorously). What is the best way to average the evalues (or bit score, whichever is easier) of the HSPs in...
View ArticleIs There An Explaination For Each Of The Pieces Of Blast Output?
I was wondering if there was full explanation for each of the pieces of this part of the output. Lambda K H 0.328 0.141 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties:...
View ArticleStandalone Blast Issue
Dear all,I have recently installed blast-2.2.26 on my machine (running MacOS 10.7.3) and I tried to perform a BLAST search using a single protein sequence as query and a formatted (by me) database...
View ArticleWhat Is The Algorithm Behind The Sequence Comparison In Uniprot Or In Any...
Hi, This is Shrujan, i wnat to know the algorithm behind the Sequence comparison in Uniprot or in any other database, which does BLAST. I need your valuable suggestions and guidance.Thanks &...
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Configuring Path To Point To The Bin Directory Inside The Ncbi Folder After...
I can't seem to get Terminal to accept the syntax described on NCBI's help page regarding configuration of the standalone BLAST installation. Here's my syntax and the error messages:
View ArticleHow do I blast against a specific portion of the nr database?
I would like to blast my sequences against the swissprot database, using local blast. For the purpose of downstream applications, I would like to do this using the copy of the swissprot database from...
View ArticleHow To Prove An Ortholog Does Not Exist In A Given Genome?
I am wondering what is the best way to prove that an ortholog is absent (or at least un-identifiable) from a given sequenced genome.My initial thought goes to a tblastx search, where an absence of...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
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