Fastest Protein Sequence Similarity Search Algorithm
I heard of RapSearch2 which claims to be must faster than blast and HMMER which is as fast as Blast. I am wondering if there is any benchmark of such programs since the RefSeq/TrEMBL sequence database...
View ArticleAlign Multikb Contigs Of A Mammalian Genome Against List Of Mammalian Genome...
I would like to be able to align multi-Kb contigs of a non-assembled mammalian genome against the list of available mammalian genomic assemblies. I would like to do this locally since I have got many...
View ArticleBiopython: Executing Blast On Custom Db
Ok, so I am using the NcbiblastxCommandline wrapper to execute a BLAST search on a custom database. cline = NcbiblastxCommandline(cmd='blastx', query=temp_path, out=blast_path, subject=path, outfmt=5,...
View ArticleExact Matching With Bowtie, Blat And Blast+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, _e.g._: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa...
View ArticleE Values Using Blastp In Biopython
Is there a reason for the E Value to differ when using BLAST on the web and using BioPython? My understanding is that these are the same source, so I am unable to understand the following differences....
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleMegablast, Makembindex, And Choosing Nmers
I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18. It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when...
View ArticleAnnotating Rna-Seq Data Using A Reference Genome.
I have RNA-seq reads from a non-model organism. I used cufflinks to identify transcripts. Is there an existing pipeline to BLAST these transcripts to a model organism's proteins to identify orthologs?
View ArticleAbout Blast Scores In Matrix Format.
Hi All, How Can I get local Blast score in matrix format??( I have score but I need in Matrix format) How can I run blast of 200 sequences in order to alignment sequences by writing a python...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
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 ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleBlast 2.2.24+ Database Error
When running local BLAST on a big database (all human proteins) I get the following error:proteinsApplicationError: Command 'blast-2.2.24+/bin/blastp.exe -query "query.fasta" - db...
View ArticleGetting Exact Number Of Genomic Copies For A Specific Sequence
Hi all,I'm trying to retrieve a set of sequences that can be used for primer design. These sequences have some requirements, e.g. present in 4 different species, not present in a number of species on a...
View ArticleRaw Alignment Score Calculation
Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.After I've now a little more understanding I can ask more specific questions such...
View ArticleBl2Seq/Blastall And The E Value Help
I am using bl2seq(2.2.25) to blastn two fasta files. I am not sure I fully understand how the (-e) parameter works. I thought the -e parameter was a cut off e-value and would therefore show all results...
View ArticleStandalone Blast Issue
Dear all,I have recently installed blast-2.2.26 on my machine (running MacOS 10.7.3) and I tried to perform a BLAST search using a single protein sequence as query and a formatted (by me) database...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
View ArticleBlast Database For Bos Taurus
Hello To All,I want to blast my sequence Only in Bos taurus database Using local Blast (Blast+). But I don't know which database I should use for this from this...
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