Customize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
View ArticleRetrieving Protein Structures
I want to make structural analysis of lysosomal proteins found in mammals. To make start, I would like to retrieve as many structures as possible from the biological database (PDB). These structures...
View ArticleTool: All-in-one NCBI / EBI / Amazon BLAST workstation
ngKLAST provides a convenient way to access and use remote BLAST servers available from NCBI and EBI web servers, as well as NCBI BLAST machines running on Amazon Cloud. The software provides a...
View ArticleExtracting the from Blast xml output using Biopython and saving in .csv
Hello, I have the blast output in .xml form and I want to retrieve few attributes like <hit_def>. I found the parser on biophython. CODE: from Bio.Blast import NCBIXML blast =...
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 ArticleHow 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 ArticleRna-Seq Contaminants Assembling Likelihood
Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I isolated those reads via taxonomical binning, what is the...
View ArticleBlast RNA nucleotide sequences with Protein-RNA complexes
Hi,I have two datasets - one folder containing nucleotide sequences of different only RNA proteins and the other folder containing different protein-RNA complexes (all FASTA files). I want to blast...
View ArticlemiRNA -identification animal
Currently I am predicting miRNA in animal.. when I perform BLASTx, i dont know how to select the non-coding protein? plz help me.. Do we have any other softwares or tools to remove coding protein??
View ArticleMpiblast Vs Blast+
How up-to-date is mpiBlast compared to blast+ from ncbi? I am not sure what the relation ship between mpiblast and blast+ is, is mpiBlast derived from blast+. blast+ seems to be multi-threaded, but I...
View ArticleBLAST Database error: No alias or index file found for nucleotide database
Hi - I am trying to run blastn, and then also SIFT standalone. I am having database configuration issues however as I am getting the following: arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b $...
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
View ArticleAfter Clustal analysis and MEGA analysis how can I obtain the probable...
I did my blast search with protein sequence of interest and then aligned it using Clustal w, did phylogeny analysis using MEGA 6. Now how can I obtain the amino acid sequence of a probable ancestor of...
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 ArticleHow To Make Statistics Of Mismatch And Unpairing Positions Between Mirnas And...
Dear all, i need to make statistics of mismatch and unpaired positions between miRNAs and their targets. What I have done is that I performed patscan and identified miRNA targets using various patterns...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View ArticleWhat to use for a measure of distance between two sequences?
I've got a lot of genetic sequences and I'd like to use various clustering algorithms on them, but this requires a measure of the distance between two sequences. I've used BLAST+ and the...
View ArticleHow To Get Number Of Hit For A Query??
hi , i'm using biopython to parse my blast xml output i make condition print on the number of for query. i print my query and sbject if the query have only one hit. but it's not working here is my...
View ArticleErrors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
Dear friends: I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity. my...
View ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
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