How Can I Get Older Versions Of Psi-Blast Program?
Hi,Do you know how I can get older versions of PSI-BLAST.Right now, I've downloaded 2.2.26, but I need to use these parameters. (Pardon me for the irrelevants). blastpgp -i seq-file -Q...
View ArticleRunning Blast On Amazon'S Elastic Mapreduce
Hello, I need to extract 10 million (yes, 10 million) sequences from the blast database -nt using the blastdbcmd command. Needless to say this will take days on my rinky-dink desktop ( In an earlier I...
View ArticleFinding The Gene Annotation Output From Web Blast In The Xml Etc. ?
Hi, I'm new to bioinformatics and am still learning how all the public databases interconnect so please bear with me :) I have de novo assembled a set of bacterial genomes, located and extracted...
View ArticleI am running blast over internet using biopython but its giving connection...
import Bio import csv from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW q_id = [] with open('C:\Users\Nadia\Desktop\imran-sequenceIDs.csv','rb') as f: reader=csv.reader(f) for row in...
View ArticleWhy Does Blastdbcmd Produce The Error: Oid Not Found
hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fastaFor...
View ArticleTrinity/Rsem/Edger Pipeline...Now What?
HI people,I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...I basically have 3 sample condtions -with 3 replicates...
View ArticleFind Genome Source From A Blast.
Hi, I've made a blast with the sequences from a plant's transcriptome which don't match to our genome. We want to know where they come from to try to improve our genome. The problem is that I have...
View Article[Help]: Extracting Sequence From Fasta Using Blast Informations?
Hi there! This is my first post on your forum and I hope you'll be able to help me. This is my first intership in bioinformatics and I'm kind of learning everything by myself. I learnt how to use...
View Articleblast -F F equivalent in blast+
In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false)In blast+ I couldn't figure out the...
View ArticleStandalone Blast problem
HI want to blast the sequences against my own database... So I am using standalone blast utility. while using update_blastdb.pl I have come accross the error of "Failed to connect to...
View ArticleCreating An Rpsblast Database From An Hmm Profile Library
I have downloaded the HMM library file from CATH and would like to convert it to a rpsblast database.Therefor, I think I need to do the following steps:Extract the HMM profiles from the library (this...
View ArticleBlast more thn several DNA sequences
Can we blast several DNA sequences against whole genome simultaneously? If yes, thn How?
View ArticleStrange "Error: OID not found" in NCBI's blastdbcmd
I'm getting a OID not found when executin blastdbcmd. My file is as follows:>cat data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted | grep scaffold00001_37_1_21>scaffold00001_37_1_21 And...
View Articleblast execution in linux
Hi all,I've recently install the ncbi-blast-2.2.30+ on ubuntu based on its user manual, but when I'm trying to test it with the blastn -help command, it says: The program 'blastn' is currently not...
View ArticleIdentifying Viral Sequences In Next Generation Sequencing Data
I am attempting to find viral sequences in the RNA seq data of sequenced tumors. Currently I have changed bam files into fasta files and have used the refseq viral dataset from NCBI, formatted it as a...
View ArticleBlast Params : Word Size, Gap Existence, Extension Penalties
I have just started Biopython and require some assitance. Using 'NCBIWWW.qblast' function (or any other); how can I set the word size and gap existence,extension penalties for BLASTp? Thanx in advance.
View ArticleError Running Blast2Sam.Pl
I am trting to convert blastn (from blast-2.2.25+) output to sam format using samtools "blast2sam.pl" script.Any suggestions to rectify the error?Error message:Use of uninitialized value in subtraction...
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 ArticleTO BLAST LARGE QUERY SEQUENCE AT ONE TIME
hi community, i have near 4000 query sequences that i need to BLAST inorder to find homology. to do this should i need to blast my query sequence 4000 times individually one by one or we have any...
View ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
View Article