I Do Get Blast Hits, But The Mapping Step (For Some Hits) Returns No Gos
In blast2go I do get blast hits but the mapping step (for some hits) returns no GOs. and also after annotation some mapped hits, hasnt any annotation (they stay green). And I have to tell you, the...
View ArticleProtein Sequence Alignment
I want to know how to call Blast from java code, I have wildtype residue, mutant residue, position of mutation, and protein sequenceI want to calculate the frequency of wildtype residue, mutant...
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleAssemble Reads According To Blast Result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
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 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 ArticleHow Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
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 ArticleBioperl Has Different Behaviours In Parsing Blast And Blast+ Result
When I was using BioPerl to parse the blast results, I found that it can parse the blast(2.2.21) result but not the blast+(2.2.25+) result(all were in the default format). The parser.pl code:...
View Articleproblem running Blast
Hi! I installed Blast in my computer, but I'm having troubles to use it.I want to Blast my protein sequence against nr database using the -remote option. Here is the command I'm using blastp.exe -query...
View ArticleBiopython Ncbistandalone Blastall Gives Different Result Than Calling...
So, first I tested what results I should get from the blastall program using the command line, with e-value 0.001:C:\Niek\Test\blast-2.2.17\bin\blastall -p blastp -d...
View ArticleBLAST database files
After I run makeblastdb against a fasta file, I get nhr, nin, nog, nsd, nsi and nsq files.Questions1) What do these file extensions mean?2) Do these files replace the original chrY.fa file which was...
View ArticleBlast With Amazon Ec2
Does anyone have any experience running BLAST with a local blast database on Cloud Bio-Linux through the Amazon EC2 infrastructure?I would love to hear how it turns out and is it worth the cost?
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 ArticleBlast Motif With Regular Expression ?
Hi there =) Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the...
View ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
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 ArticleWhat Program Or Database To Use To Analyze Blast Result Output?
Hello, I ran the blast locally and got the blast output like followingquery1 gi|4003386|dbj|AB020866.1| 98.44 64 1 .. query2 gi|60834728|gb|AY894071.1| 92.11 76 2 ... query3 gi|21618453|gb|BC032801.1|...
View ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
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