Problems 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 ArticleBlast Db Version
Hi all,I'm currently updating my BLAST application from the legacy BLAST to BLAST+. It seems that BLAST+ expects 'version 4' database files. Which my blast DB's apparently are not.Is there a way to use...
View ArticleBlastclust Ignores The Multithreading Argument (-A)
I'm trying to run:blastclust -a 48 -p T -d ./uniprot/2011_04/all.fasta -v progressI have 48 cores on the server thus -a 48 argument, but only 100% CPU (1 core) is used.I have Blast2 version 2.2.21...
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 ArticleHelp needed for local Blast2GO Database Installation on Mac system
Hello and good day everyone, I'd like to install local Blast2GO database into my desktop. It is mac os x operating system. I already followed the 'Step-by-Step Description' provided on the blast2go...
View Article(Determine If Necessary And) How To Realign Blast Results For Arlequin?
I am newbie in bioinformatics, and now trying to learn about alignments, so sorry about the lack of vocabulary. After blasting a sequence, this is my output from a BLASTN... lots of other aligns ......
View ArticleMakeblastdb Error
I get this error when trying to make a database from fasta file:BLAST options error: blastdb.FASTA does not match input format type, default input type is FASTAhere is sample of my...
View ArticleHow to create 10GB blast database
Hello.I want to create a database for local blast but fasta file with reads is 9Gb. So i want from this file to create only one database for the blast and not many files. So i put -max_file_sz argument...
View ArticleWhat Is Score Bits In Blast?
i want to konw that what does it mean score and bits in local blast output from the following example?'. Score = 38.2 bits (19), Expect = 0.11 Identities = 22/23 (95%) Query: 1 cttaacttcagctacctcgagta...
View ArticleFind All Similar Sequences In Genbank
Hi, I would like to get a feel for how many sequences related to my virus of interest are available on GenBank. I am thinking about using a recursive BLAST approach. Start with one genome, BLASTn, and...
View ArticleError with database alias when running blastp
I have made a blast protein database with this command:./makeblastdb -in input.fsa -out prot.db -dbtype prot -hash_indexIt has generated 8 files as follows:prot.db.phd prot.db.phi prot.db.phr...
View ArticleComparable E-Value Among Blast Programs
If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be...
View ArticleBlast Settings For Short Sequences
I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:>ponzr CGCGGTAAAACACATTTG And...
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 ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
View ArticleTblastn Chromosome Database Download
On the NCBI web interface for tblastn, one of the database search options is the "chromosome" database. Title: NCBI Chromosome Sequences Molecule Type: Genomic Update date: 2012/09/20 Number of...
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 ArticleBlast Multifasta Against Ncbi Nr Database, And Download All The Results
Hello, i have a fasta file with 7600 nucleotide sequences, i have a local nr database formated for blast, with makeblastdb, i don't use formatdb because it give errors (zero length sequences). I blast...
View ArticleSelect Sequence From A Psiblast, And Launch A New Iteration From It
I would like on my local machine or remotely if it is possible too, launch a psiblast from a sequence. Then, like on the website of ncbi, select my own sequences from the result file. And launch...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
View Article