Local Blast Question About The Genome Download
Hello All,I have trying to go local blast for my genes (55 in number). I need to find the genes in all the mammalia class. I was trying to download the genomes for all the species of interest but I...
View ArticleWhere To Download Pyzerg Wrapper
Do you known where can I download PyZerg becouse the address http://bioinf.scri.ac.uk/lp/programs.html does not longer existsIs listed herehttp://biopython.org/wiki/Scriptcentral
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
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 ArticleMakeblastdb Error
I ran into the following error when trying to build a database using makeblastdb (NCBI BLAST 2.2.23+).> makeblastdb -in uniprot90.faa -dbtype prot -parse_seqids Building a new DB, current time:...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleNcbi Blast Failing For Unknown Reasons
I have a Python script that runs BioPython's Web Blast function. We're using large fasta files, so the script breaks these files into smaller files and then blasts them. Below is a partial...
View ArticleStrategizing Blast Result Parsing
I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you can imagine, my blast results for this dataset are redundant in the...
View ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
View ArticleRun Multiple Sequences Through Psipred
Hi, I have psipred working (thanks to some posters on here) and can confirm it works for single sequences - however when I input a fasta file with multiple sequences it only gives the output for the...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for 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 ArticleGATK BaseRecalibration report
hi everyone I use GATK to do snp call. But I don't understand the BaseRecalibration report as follows . And i really don't known the word 'Observations' 'Errors' stand for. Thanks in advance RaedGroup...
View ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
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 ArticleBlast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
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