Blast Contigs To A Reference Sequence And Obtain An E-Value
Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align...
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 ArticleRunning Blast With C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
View ArticleError When Using Makeblastdb On A Large File
Dear All,I have created a stand alone blast on my system, to work with NGS data and it is working fine. However, I have got a sequence file which is about 2400MB, which is two large to create a local...
View ArticleFinding Protein Homology?
I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?I'm...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleFind protein homologs with BLASTp
I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90%...
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 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 ArticleOutput File Format "6" - Blastplus - Gene Name ?
I am working on a second design for a sequence capture array (similar to a micro-array, but with genomic DNA) and I want to blast a few sequences that seem problematic in my design. The sequences are...
View ArticleEquivalent Blast And Blast+ Commands
Hi all,I used to use an old blast version (2.2.21) and now I'm moving to the latest blast+ version (2.2.25). The thing is I don't know which options in the 2.2.25 version are the options equivalent to...
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 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 ArticleParsing Blast Results For Different Genus
Dear All,I have obtained several .gb BLAST results that I want to split in different .gb or .fasta files accordingly to genus.I searched for different ways to do it in the web, but didn't find a way to...
View ArticleHow Can I Sort Blast Output Based On E-Value?
Hello: I have a blast output with about 50000 sequence list. The problem I have is that I need to sort those results based on the smallest e-value to greater e-value. Could you guys please suggest me...
View ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
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 ArticleHelp With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
View ArticleUsing Ncbi-Blast-2.2.25+ Remote Flag. Where Can I Find The List Of Databases...
Hello.I am trying to blast using -remote flag to use the databases on the remote server. The problem is I don't know the name of the datbases for the -db flag. Is there any website where I can get the...
View ArticleReduce Blast Xml Size?
Hi, I have a really large BLAST XML file - something like 30gb in size. I'd like to reduce it so I can run through it quicker with Biopython. Is there a way to reduce the file by keeping something like...
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