How To Find Sequences With A Given Number Of Mismatches
Hi! Is there any script or tool that allows to find similar sequences given the maximum acceptable number of mismatches? What I want is something similar to a Blastn search, but instead of filtering...
View ArticleAssessing Quality And Accuracy Of De Novo Genome Assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
View ArticleHow To Use Biopython To Parse Blast Output And Get Gene Symbol From Ncbi?
Hello all. I am very, very new to Python/Biopython and am currently stuck.I am using standalone BLAST via Bash. I have about 40k non-human sequences which I am blasting against the human genome,...
View ArticleFinding 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 ArticleAlignment Matrix
Dear all,I have a problem with the following website:http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096More specific, I have a problem with the matrix (completely...
View ArticleBlast Against Swissprot Db
Hi I downloaded the swissprot database and used the command formatdb and then tried blastx against this database, I used the command: megablast -b 1 -T T -i....results.html I received results but with...
View ArticleHow To Prove An Ortholog Does Not Exist In A Given Genome?
I am wondering what is the best way to prove that an ortholog is absent (or at least un-identifiable) from a given sequenced genome.My initial thought goes to a tblastx search, where an absence of...
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
View ArticleIs There Any Api Of Blast And Uniprot To Align Protein?
Given a set of protein's gi/UniProt identifiers. I want to find the e-value/identity between each of the pairs. I decided to do it by program but I cant find any apis of Blast and Uniprot. Any ideas?
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
View ArticleAligned Ranges In Blast
I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched. As far as I'm aware, the standard output only gives this...
View ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleNcbi Blast Two Parameters'S Question
Hello, I don't know NCBI BLAST two parameters, here they are: -num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Default = `500' -num_alignments...
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 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 ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
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