Blastn And Blastcmd Issues - Blast
Hey all, first of all I'd just to say that I am fairly new to the field of bioinformatics and I'm, unfortunately, learning by my mistakes more than my successes atm and I'm having some trouble...
View ArticleWhat Substitution Matrices Are Available For Blast?
I'm having trouble locating documentation on what substitution matrices are supported by command-line BLAST+ tools. Do they have a specific set of matrices built in? Are they hidden in a directory...
View ArticleShow Progress (Bar?) For Blast+ Query
Hello everyone,It is possible to visualize the progress of a local blast+ (verbose mode or something [maybe python ou perl])?Thanks in advance!
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
View ArticleHow To Get Ungapped Sequences From Blast Output?
I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this:result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap")...
View ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View Article. [Blastall] Warning: Unable To Open Bos.Db.Nin
I created the database of 1 chr using makeblastdb tool of localblast. It showing me output, But it also showing me warning while i am blasting from programming. that ..[blastall] WARNING: Unable to...
View ArticleBlast E Value Calculation
I'm trying to work out the formula for BLAST e value calculation. I have surfed all across the internet looking for it, but the only thing I'm able to find is the formula provided here:...
View ArticleIs there a good service for annotating transcripts?
After getting say 100k transcripts from an rna-seq project, generally one wants to annotate them against a database like nr, using say blastx. Problem is, this is very slow, taking e.g. a week with 24...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleLocal Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
View ArticleProblem With Interpretation Blast Results
Hi, I'm struggling with BLAST. I'm not sure if I can properly interpret the results of BLAST. Can anyone tell me when I can be sure that the sequences of the proteins are enough similar to be...
View ArticleCommand blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
View ArticleBlast - problem with xml output
I encountered a weird problem when I used blast(i'm using blastall 2.2.26). I have a fasta file with 8 sequences and I'm running blast on it to get the xml output, the problem is I get 1-8 iterations...
View ArticleHow Is The Score And E-Value Calculated In Blast Outputs
Hi!I am working on a BLAST similar tool and wanted to implement the Score (raw Alignment score) and the E-value. I was wondering if someone could please explain me how it is calculated by showing it...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
View ArticleDifference Between Blastall And Blastn?
What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?Are the results supposed to be the same in terms of...
View ArticleBlast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
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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