Orf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View ArticleLegacy Blastx Output (Karlin-Altschul Statistics) From Xml Output
If have to generate legacy blastx output from Blast XML output (why do people still require this!!!?). The legacy output has a block starting with Score E Sequences producing significant alignments:...
View ArticleThe Same Sequence Occurs Multiple Times In Blastp Output
Hi there,I am using blastp (using blast+ 2.2.25) to align bacterial proteins (in the file multiple_queries.fasta) against a custom database (genome.db) containing all proteins coded by the genomes of 6...
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
View ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View Articletranslational genomics using synthenic relashioships
hello, I want to map some sequences on a genetic map (the genome of the target organism is not sequenced, so it's like putative positions) using a closely related organism with a sequenced genome....
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
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 ArticleExtract Unmapped Reads From Blast
Is there a way to tell blast to output the unmapped reads into a separate file or at least the name of the unmapped sequences?
View ArticleProcess tabular BLAST output
Dear all,Iam struggling with processing tabular BLAST output. I would like to do the following:Take a Blast output table (simplified):Sequence ID | e-value | GISeq1 0.001 12345Seq1 0.001...
View ArticleShortlisting Genes From Various Gene Prediction Methods Based On Blast Results.
Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
View ArticleProblem with extract aligment from a blast result to a fasta file....
I have a metagenome like a db, and i need to blast a genome with this metagenome, the results are veryy wide, and i need to extract the aligment from this result and put into a fasta file, but i cant,...
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.
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleHow Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
I'm looking for a way to do BLAST simultaneously with >1 sequence. The input is several fasta files or one file containing several sequence formatted in fasta. For an initial testing, I want to try...
View ArticleHow To Define And Calculate Cip ( A New Parameters For Blast Analysis Of Cip...
IN the paper “Improved criteria and comparative genomics tool provide new insights into grass paleogenomics " they said:To increase the significance of inter-specific sequence alignments for inferring...
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