How Can I Batch Blast Sequences To Identify Them?
I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but...
View ArticleProblem with blastp when blasting against custom made database
Hello, I have been trying the last days to make my database for blast work but I really don't know how to figure out this problem. Begining from the start of the problem, I want to make a blastp...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
View ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
View ArticleRna-Seq Contaminants Assembling Likelihood
Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I isolated those reads via taxonomical binning, what is the...
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 ArticleExtracting Fasta Alignments From Parsed Blastxml File
Hello, I have cobbled together a small script that parses a BLASTxml file. It seems to parse the xml file just fine (judging from what it prints to the screen). The problem is the hsp.fas alignment...
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 ArticleParse Blastdb Format From Java
Does anyone know a java library to parse blastDB files? I've found the specification at http://selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html for the file format, and the code for a C...
View ArticleTool to map sequences and get genomic coordenates
Hello, Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the...
View ArticleStarting Point
I am trying to get into bioinformatics or just trying to get a jist of what is going on. I wanted to see the difference between different methods for gene variation. I looked at blast and installed it...
View ArticleProblems With Biopython When Running The Ncbistandalone.Py Program
Hi, I am having problem while running NCBIStandalone library of biopython. i want to retrieve sequence titles from output of blast but it gives error on iterator. Following is the code to retrieve...
View ArticleCompare Two Protein Sequences Using Blast On Biopython Without Making A File...
Hi guys, I have been trying to do this, but I've got stuck. I know how to blast two sequences using biopython and the standalone Blast, but I make files in order to blast them. I think making files...
View ArticleBlast2Go Doesn'T Work With My Fasta File
Hi all, i downloaded human unigene fasta file from Here (Hs.seq.uniq.gz with .uniqe format), and change it to .fasta by notepad. when i submitted the file to blast2go it doesn't work and give me an...
View Articlebowtie, tophat vs BLAST
Hi, I have a very basic question but it confused me a little bit. For a metatranscriptome data, we can compare it with the NCBI prokaryote genome collections. Shall I use bowtie, tophat these kinds of...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleMCL Clustering for Large BLAST output files
Hello,I have pairwise blast result for more than 400 bacterial genome each genome has more than 5000 sequences. I want to cluster the similarity information using MCL to identify protein families....
View Articleblastn for short sequences
Hi everyone,I was trying to use blast to map short sequences (between 15 - 30 nucleotides long) to the human reference genomeI have blast locally installed:these are the options that I used:blastn...
View ArticleProblem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
View ArticleBlast K and Lambda
Hello, I have a question about Blast parameter. In Blast search results, for different queries the K and Lambda value is different for Ungapped search. For gapped search , they are the same.However,...
View Article