Strategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View ArticleProtein Sequence Alignment Using Blast
Hi All, I am trying to run Blast over protein sequences from two organisms. I downloaded the fasta from NCBI. I am trying to iterate over the list of sequences in the fasta file and do a sequence...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
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 ArticleTool: Beta testing bioinformatic tools
Hello! I am looking for beta testers for three bioinformatic tools I have written. They include a sequence alignment tool, a primer search and design tool and a small helper tool for the lab. If you...
View ArticleCompute Blastx E-Value
Does anyone know how blastx e-values are computed? Is it the same as blastp, except the query sequence is divided by 3? I've tried using E = (m/3)n2^(-S), but I get slightly different results than from...
View ArticleCreate Blast Database From Query Result?
Possible Duplicate:make a custom BLAST library using the output of another blast result Hello, I would like to create a BLAST database using as input a file generated after executing a BLAST query. I...
View ArticleHelp needed for local Blast2GO Database Installation on Mac system
Hello and good day everyone, I'd like to install local Blast2GO database into my desktop. It is mac os x operating system. I already followed the 'Step-by-Step Description' provided on the blast2go...
View ArticleHow To Extract Max Score Blast Hit Among A Huge Data Set?
Hi everyone, I want to extract max score blast sequence among 50 genomic data set : my approach like this:I did all the denovo assembly of all 50 genome.Next i predicted all the ORF using Prodigal: (A...
View ArticleHow To Extract Max Score Blast Hit Among A Data Set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
View ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View Articleeach protein with each protein
Dear colleagues,I have a lot of proteins. What is thesimplest way to compare each oneof them with all the other proteins?Probably I have to make a databaseand use a program like BlastP.But how to make...
View ArticleProblem In Making Blast Database (Makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
View ArticleShow Progress (Bar?) For Blast+ Query
Hello everyone,It is possible to visualize the progress of a local blast+ (verbose mode or something [maybe python ou perl])?Thanks in advance!
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 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 ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
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 Articleblastn cannot find the database
I'm new to BLAST and am trying to run a legacy blast command using blast+. I have downloaded the human_genome databases and unzipped and untarred them.The databases are in:...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
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