Comparing Protein Datasets By Sequence
Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins between each dataset pair.I want to identify...
View ArticleWarning Unable To Open .Nin
I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux. I created the database for Bos_taurus using Formatdb commamd of...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticleNews: NCBI BLAST URL domain changes to take effect December 1, 2014
As of December 1, 2014, BLAST searches sent to the www.ncbi.nlm.nih.gov/blast URL will not function. The officially supported URL domain for BLAST searches at the NCBI is blast.ncbi.nlm.nih.gov. Please...
View ArticleMakeblastdb Can'T Find My Fasta Files
I'm trying to make a nucleotide database for my sequences. After opening C:Program Files\NCBI\blast-2.2.28+> in the command line, I typed in makeblastdb -in test_gene.fsa -parse_seqids -dbtype...
View ArticleConverting Blast Results In Fasta Format
Hi, I "blast" my protein sequence against the NCBI database and I wish to save the returned results in FASTA format. Is there a way to convert the sequences all into FASTA format and save them or do I...
View ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
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 ArticleLooking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
Hi allI am building a pipeline for taxonomically identifying a blast result at each taxa level, with a bespoke reference dataset. I want it to be easily reproduceable, which it is, other than an ugly...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleNcbi Refseq Viral Genomes
I want to create custom blastdb with all viruses available in the refseq. But I don't know which source files to use. My first point is:ftp://ftp.ncbi.nih.gov/genomes/Viruses/From research I concluded...
View ArticleTool: All-in-one NCBI / EBI / Amazon BLAST workstation
ngKLAST provides a convenient way to access and use remote BLAST servers available from NCBI and EBI web servers, as well as NCBI BLAST machines running on Amazon Cloud. The software provides a...
View ArticleIdentify Contamination With Blast
Many reads from a recent RNA-seq sequencing run I had done are not mapping to the reference sequence they had come from. I converted some of the sequences to fasta format, and blasted them against NR...
View Articleeffective length of query in blast
Dear all,I don't understand the meaning of effective length of query in Blast which is used in calculation of e-value.Can anyone explain it to me?Regards
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
View ArticleHow to add additional common names to a blast database
blastn with nt as a database can also return scientific name and common name of the blast hit viasscinames and scomnames in outfmt.I can get that also if I make my own blast database if I add-taxid_map...
View ArticleNcbi Blast Output Missing Subject Name
I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for...
View ArticleBlast Database For Bos Taurus
Hello To All,I want to blast my sequence Only in Bos taurus database Using local Blast (Blast+). But I don't know which database I should use for this from this...
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 understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
View Article