Ngs Multi-Dataset Analysis
Hello I have some doubts on my analysis of an 454 EST s assembly of data that come from 3 different datasets. Each dataset come from the same organism, but in different conditions (resistance to...
View ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
View ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
View ArticleHow To Blast Consensus Sequences With Bacterial Genome?
Dear all,Subject- To find number of hits available for the particular consensus sequence in bacterial genomeI am having this consensus...
View ArticleThe Meaning Of The E In Blast Output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
View ArticleHow To Concatenate Blast Results (M8) Via Setting Threshold Of Distance...
hi, dear guysI performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance. however, these hits have no...
View ArticleWhat Exactly Does Formatdb Do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
View ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
View ArticleWhy Does Blastdbcmd Produce The Error: Oid Not Found
hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fastaFor...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
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 ArticleHow To Get Status Update In Ncbi Standalone Blast?
For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any...
View ArticleProtein 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 ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleBuilding Protein Models From Tblastn Tabular Format
Hi,I have done tblastn and now I have a blast tabular output format for proteins. Each hit has this informationqueryId, subjectId, percIdentity, alnLength, mismatchCount, gapOpenCount, queryStart,...
View ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAG DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCY TTAEIVRKEKLCYVARMQKEITAPSTMKIKI KEITALPSTMKIKII... ...I need to...
View ArticleQuick Command To Split Large Blastx Files?
Any thoughts? I have large 7 gb files as resulted from Blastx any clue how to split them?Edit:These are standard blastX files (fasta). I need to split them for a program (binning) call SOrt-ITEMS/MEGAN
View ArticleHow To Search Blast With Ensg Id'S?
I have some ENSG id's and I would like to search BLAST database with this id's. When I use the ENSG id's directly, BLAST cannot find any genes. I think I need to convert the ENSG id's to some other...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
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