Finding 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 ArticleWeb Blast Apache Configuration (Error 403)
Hi, I'm trying to run Web Blast 2.2.28+ locally trough Easy PHP Dev Server 13.1 (Apache 2.2, Windows 7), but when I click on search it shows ERROR 403 when I open it within my site or the following...
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 Articlestart and stop position of mapping in Blast
I used makeblastdb to search many short fasta sequences in a known organism. I successfully completed this step and got the mappings. My question is1. how can I get the start and stop coordinate ?for...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
View ArticleBlast2Go Graphs
I perform blast in the blast2 go and then the GO and annotation steps. In previous projects I had the option to create "direct Go count" graphs on the process, function and component. I remember that...
View Articleabout Blastx generated file
Hello, i used blastx blasted my query file with a protein db file. my query sequences more than 140000, so i just want to see aligned query sequences. but the result gives all the query , and their...
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 ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
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 ArticleHow To Scale A Pssm For Ncbi Blast
Hi again,I'm trying to do a local NCBI BLAST search using the PSSM of a conserved CDD domain (.smp file in the database, cave LARGE file).My database is containing nucleotide sequences and the PSSM is...
View ArticleWhy Is Makeprofiledb Throwing Confusing Defline Errors?
I have an alignment file [alignment.aln]:>lcl|21974 MRLQLILTITLLLTSFMGYRDAAVIQGKTERSAMKMRKLLQILHKNSCGCNDDDSDGDDCCFGTCLDNACWPVKKRSSAII can make a blastdb with this file:makeblastdb -in alignment.aln...
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 ArticleBlastp Against Human Proteome
Hey guys,I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans. I will run the...
View ArticleHow To Differentiate Databases When Blasting From The Command Line?
Hello, I'm creating a python script to take each ORF from a genome and blasting it against 3 other genomes in order to retrieve common and unique ORFs for the query genome. I am using Bio.NCBIXML to...
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 ArticleHow To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or...
We have a 23 nucleotide CRISPR target sequence of which I would like to find out if it also present in other locations in the genome. The sequences directs a CRISPR RNA construct to introduce a indel...
View ArticleRFAM problem. Died at rfam_scan.pl line 281, line 1128517
Hi everyone. I am working with RFAM. It is blocked in some line with three different commands.perl rfam_scan.pl -blastdb Rfam.fasta Rfam.cm 200pb_Pamicro.fasta --nobig -o rfam_200_nobig.out Died at...
View ArticleHow to analyze the ProDom output? I have some results to support the...
Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of...
View ArticleMissing BLAST hits - max_hsps and max_target_seqs?
Hi, I have a single file that contains 10,000 query sequences, each 300bp long. The subject is a single chromosome that I have imported into a nucleotide database ("makeblastdb -dbtype nucl"). Due to...
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