How can we find mature 3p sequence in precursor miRNA through insilico mining
How can we find mature 3p sequence in precursor miRNA through insilico mining.......? eagrly waiting for answer expecting helping hands
View ArticleFrom Sequence To Gene Id
Hi,I have around 10000 fish EST sequences in a fasta file and want to have an Entrez gene ID for as many as possible of these sequences. The reason I want Entrez gene IDs is to facilitate gene ontology...
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 ArticleHow To Use To Use Standalone Blast In Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short...
View ArticleStrategies 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 ArticleCompare Two Protein Sequences Using Blast On Biopython Without Making A File...
Hi guys, I have been trying to do this, but I've got stuck. I know how to blast two sequences using biopython and the standalone Blast, but I make files in order to blast them. I think making files...
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleForum: Looking For Help To Understand Bioinformatics Papers On Blast, Yasara...
Hello, I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done. I only have to write about BLAST, YASARA and the huntington disease...
View Articlegetting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleRead Blast Output Directly From Stdout With Bioperl
Hi there,I finally decided myself to try Perl for a project and I got a question concerning BioPerl. I would like to read the result (blastxml) of a blast query directly from STDOUT. Is it possible...
View ArticleWarning Unable To Open .Nin
I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux. I created the database for Bos_taurus using Formatdb commamd of...
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 ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleFunctional Annottations From Blast.
Hello, I'm writing a program that takes sequences in some format (FASTA for example) performs a BLAST search on it and takes a funcional annotation of each result, then looks in Gene Ontology database...
View ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleBLAST definition and difference between 'qcovs' and 'qcovhsp'
Hello,Can anyone provide a clear definition of what exactly the BLAST+ output parameters 'qcovs' and 'qcovhsp' are? From the help pages:"qcovs means Query Coverage Per Subject""qcovhsp means Query...
View ArticleMakeblastdb Error In Blast+ 2.2.26
I am running makeblastdb from blast+ version 2.2.26 on uniprot_trmbl.fasta and get the following errorBLAST Database creation error: Error: Duplicate seq ids are found: GNL|BLORDID|2707210Any ideas...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
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