Best Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleMapping blast xml report elements to their variable names in biopython
Hi all ^_^ Im working on a script in biopython that extracts SSR's from some plant species , blast their sequences against each other and group the results of similarity based on some coverage value ....
View ArticleBlast more thn several DNA sequences
Can we blast several DNA sequences against whole genome simultaneously? If yes, thn How?
View ArticleHow To Get Conservation Of Vaccine Candidates Between Hundreds Of Bacterial...
Hi community,We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about...
View ArticleIn biopython, how can i get the 100% identity aligment?
I find the way to get the identity of hsp ,but no alignment.One alignment can have multiple hsp, that means the score(identity) of hsp is no equal to alignment. when i do blast in webpage, i always get...
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 ArticleStandalone Blast Options
Hi all , I'm using local BLAST to retreive the single top most hit invoking "-v" option of blastall/RPSBLAST, from the local database sequences. I'm getting the top hit in most of the cases but in some...
View ArticleCan't access individual attributes of tabular outfmt 6 blast output while...
Hi ... I'm trying to parse a blast tabular format file (outfmt 6) to access it's individual elements for further manipulation . I need to retrieve the qseqid, qstart, qend, qlen, qseq, sseqid, sstart,...
View ArticleGetting Taxonomy Lineage From Ncbi Gi Or Accession Number
Hey GuysI have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not...
View ArticleGenomic Sequences For Drosophila In Refseq
Pscan was recommended to do TF enrichment previously. RefSeq (for human, mouse, and drosophila, e.g. NM_000546) in one of the acceptable identifiers. I have a list of genes in a non-model organism, and...
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 ArticleRNA-seq for ncRNA analysis in Rice
Could anyone kindly suggest some protocols on analyzing ncRNA using RNA-seq data, articles published on identifying and analyzing Plants ncRNA will be equally of great help.Thanks
View ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
View ArticleWebtool For Fetching Pmids From Blast?
Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs...
View ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View ArticleUsing Ncbi-Blast-2.2.25+ Remote Flag. Where Can I Find The List Of Databases...
Hello.I am trying to blast using -remote flag to use the databases on the remote server. The problem is I don't know the name of the datbases for the -db flag. Is there any website where I can get the...
View ArticleBlast+ Error: Sequence Not Returned
I'm getting an error when running blastn against the nt database:Error: (117.2) CThread::Wrapper: CThread::Main() failed NCBI C++ Exception: Error: (CSeqDBException::eArgErr) Sequence not returned.The...
View ArticleHow To Filter A Blast Xml Output ?
Hello list, I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a...
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 Articleputative conserved domain in introns
I am currently working on set of long intron sequences..once I put them in to NCBI CD-search tool(CDD) those intron sequences showed that such sequences are having putative conserved domains and the...
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