Sequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
View ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
View ArticleOnline blast and standalone blast return different hits?
Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to...
View ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View ArticleMining Ortholog Cliques
Does anyone have experience working with mining cliques from ortholog data? I have orthologs generated by best reciprocal blast from 22 species. It is 21 Ensembl species with one species we are...
View ArticleHow To Extract Max Score Blast Hit Among A Data Set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
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 ArticleWays To Quantify Proteome Analysis Via Blast
I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database....
View ArticleAre There Local Aligner Like Blast Working On Unicode Characters?
I want to use a blast-like local aligner to find common substring between common human readible texts. e.g. social media data. A normal plagiarism finder won't do because the intention is to align GB...
View Articlelocal or remote blast BLASTp against pdb database (formatdb)
I want to blastp protein sequence file (>3000 sequences) against PDB database for generating templates for Homology modeling. Please help!!I tried remote blast and local blast using formatdb but...
View ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
View ArticleGetting Top 10 Sequences Of Blast Results Bio Python
Hi, I want to get top 10 sequences of BLAST results (just the sequences, no alignment or score or e-value etc). I am inputting a text file containing 5 fasta file. So my output should be top 10 blast...
View ArticleHow To Search Blast With Ensg Id'S?
I have some ENSG id's and I would like to search BLAST database with this id's. When I use the ENSG id's directly, BLAST cannot find any genes. I think I need to convert the ENSG id's to some other...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleProblem Parsing Xml In Biopython
Hi mates, I m new in python and I m trying to parse a result from local Blast...here the code.from Bio.Blast.Applications import NcbiblastpCommandline from Bio.Blast import NCBIStandalone from...
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 ArticleSetting E-Value In Blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View ArticleTo Do Blast Alignment Of Two Proteins By Biopython
I am new to biopython and I am not sure if it is a stupid question.I would like to perform the same task as the one can be done on the web based blast. I am trying to align two protein by providing...
View Article