The Same Sequence Occurs Multiple Times In Blastp Output
Hi there,I am using blastp (using blast+ 2.2.25) to align bacterial proteins (in the file multiple_queries.fasta) against a custom database (genome.db) containing all proteins coded by the genomes of 6...
View ArticleRunning Blast On Multiple Sequences At Tigr
hello everyone,Can anyone tell me how to do multiple seq blast in TIGR...thanks,Jyoti
View ArticleIssue With Alignment Of Short Dna Sequences
Can anybody inform me, in the algorithms for "alignment of short DNA sequences to the human genome" whether the repeats in genome is considered as Junk or not ? More clearly, as an example: BowTie ,...
View ArticlemiRNA -identification animal
Currently I am predicting miRNA in animal.. when I perform BLASTx, i dont know how to select the non-coding protein? plz help me.. Do we have any other softwares or tools to remove coding protein??
View ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View Articlegetting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View ArticleHow To Get The Result Which Mismatch 1 To The Query Sequence By...
the program is blastn -task blastn-short -query rfam_trimed_short_uniq.fa -db /root/bio-analysis-soft/database/gss-est-db/tage -ungapped -penalty -1 -reward 1 -outfmt 6 -out 2 -num_threads 12I get an...
View ArticleStandalone Blast Options
Hi all , I'm using local BLAST to retreive the single top most hit invoking "-v" option of blastall/RPSBLAST, from the local database sequences. I'm getting the top hit in most of the cases but in some...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleSpecific E Values In Blast Score
I have e values in one column but I want to select specific e values less than 0.0003 in order to print the same column.
View ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticleStrategizing Blast Result Parsing
I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you can imagine, my blast results for this dataset are redundant in the...
View ArticleHow To Scale A Pssm For Ncbi Blast
Hi again,I'm trying to do a local NCBI BLAST search using the PSSM of a conserved CDD domain (.smp file in the database, cave LARGE file).My database is containing nucleotide sequences and the PSSM is...
View ArticleGene Function through sequence homology
HiSo I've got list of genes putatively involved in Leptospira virulence, and I want to produce hypotheses on their function through sequence homology. So I was thinking of BLASTing them as a first...
View ArticleBash Script To Filter Blast Xml Output
I have read the instruction here:XSLT stylesheet to filter blast xml output And here:How to filter a blast xml output ? and I came up with this script:#!/bin/sh # # filterblastxml.sh : Script to filter...
View ArticleParse Web Blast Output
I have installed NCBI wwwblast at our local server and blast is running absolutely fine. I wanted to refine the html output which the blast is showing. For example, while showing alignment description,...
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 ArticleBLAST alignment score analysis
I've been evaluating a Smith Waterman implementation with ncbi BLAST and found out that for the same alignment (with no gaps) the alignment scores differ between those two algorithms. Here is the...
View ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
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