Protein Sequence Alignment
I want to know how to call Blast from java code, I have wildtype residue, mutant residue, position of mutation, and protein sequenceI want to calculate the frequency of wildtype residue, mutant...
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!
View ArticleMost Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
View ArticleBest Reciprocal BLAST and Alternative Transcripts
How sensitive is BLAST to detecting the various events that lead to isoforms of transcripts. I've had decent success in being able to capture orthologs things like nonsense mediated decay or highly...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleRunning Blast On Amazon'S Elastic Mapreduce
Hello, I need to extract 10 million (yes, 10 million) sequences from the blast database -nt using the blastdbcmd command. Needless to say this will take days on my rinky-dink desktop ( In an earlier I...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleOpening A Fasta File In Windows
Hi all,I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format and then format it using makeblastdb.then extract the first 1000 characters...
View ArticleBiojava And Blast+
Dear all, i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to carry out many blast searches from time to time, i decided to install the...
View ArticleWhy Do Blastall And Blast+ (Blastn) Give Different Results For What I Beleive...
I've recently run two searches, one with blastall (from legacy blast) and one with modern blastn. Both versions are 2.2.25 (the most recent).The blastall search is: blastall -i test.fasta -p blastn -d...
View ArticleBlastdbcmd Cant Find Protein Database
Here is the command I used:blastdbcmd -entry_batch input.gi.txt -out file.out -target_only -outfmt %t -db my_protein_database.fastaI got an error "Error: Entry not found in BLAST database". I have the...
View ArticleBlast Motif With Regular Expression ?
Hi there =) Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the...
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 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 ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
View ArticleWhy am I getting the BLAST option error: file does not match input format type
COMMAND USED: makeblastdb -in sorted_alu_seq.fasta -dbtype 'nucl' -out aluBLAST option error: sorted_alu_seq.fasta does not match input format type, default input type is...
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
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 ArticleOld Blastall Vs New Blastall
I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works...
View ArticleTo Do Blast Alignment Of Two Proteins By Biopython
I am new to biopython and I am not sure if it is a stupid question.I would like to perform the same task as the one can be done on the web based blast. I am trying to align two protein by providing...
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