Downloading Fasta Files
i need to download about 40 complete genomes from ncbi and still filter out sequences between specified bps(like btn 1000bp to 3000bp) from the genomes separately. i need help on how to do that. i...
View ArticleGNU Parallel Block Issues
Hello,I am using GNU parallel to speed up my BLAST jobs. I have seen the example outlined in the following post (https://www.biostars.org/p/63816/) and used the command: cat 1gb.fasta | parallel...
View ArticleProblems Using Formatdb And Fastacmd
Hello!!I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.I am trying to make a db from single mouse chromosome from NCBI using formatdb. Afterwards I try to obtain...
View ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View Articleclustal w result interpretation
I used microrna in clustal w software to remove redundancy . some part of output was like this ..can any one tell how to interpret the results ..... what is that score. how can i know wether the...
View ArticleBLAST: Querying a single sequence without input file in C
This is with reference to the query posted in https://www.biostars.org/p/17265/. If I try to run the following using command line it runs perfectly fine: blastn -query <(echo -e...
View ArticleQuestion Regarding Blast And Blat Function
The attached file mouseReads.fasta (Copy/pasted below) contains 67 short reads from a mouse RNA-Seq experiment. The reads were downloaded from the NCBI Short Read Archive. Millions of reads were...
View ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleCombining stats of multiple BLAST queries
Hi all,I have a FASTA file with let's say following structure:>Query_1 actgacgac....>Query_2 gtacgatcagct...I want to BLAST this FASTA file against a set of databases one by one and combine the...
View ArticleHuman Genbank Ids
I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want...
View ArticleHelp In Configuring A Local Blast Server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
View ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View ArticleE-Value Threshold Analysis
Hi, I've been experimenting with various sequence search tools and been using their E-values to compare results. One concern I've had is really how appropriate this is. For example in practice would...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleBash Script To Filter Blast Xml Output
I have read the instruction here:XSLT stylesheet to filter blast xml output And here:How to filter a blast xml output ? and I came up with this script:#!/bin/sh # # filterblastxml.sh : Script to filter...
View ArticleMultiple mapping (Taxonomy, Seed, ...) of blast(-like) tabular output
Hello, I am dealing with short sequence reads (>1,000,000 reads) from a metagenome and a metatranscriptome. I used a BLAST-like program called RAPSearch 2, which provides me with a BLAST Tabular...
View ArticleConvert Blast m8 output to XML
I've used usearch's ublast feature on my datasets. I'm now wanting to use a package such as findorf on them. However, this requires XML formatted data, which usearch does not support as output. I have...
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View Article