Gene ID conversion and Pathway analysis after mosquito blast
Hi all I have got my blast result from mosquito Contigs Fasta format. Sth like query_name query_length accession_number 1059N_ae_contig_1 676 XM_001650645 1059N_ae_contig_5 563 XM_001650988...
View ArticleEmbedding Blast Tool In A Website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
View ArticleBlast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View Articleblast against genomes in biopython
from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn","nr",...
View ArticleBl2Seq In Blast+
I have recently installed blast 2.2.24+ and I was looking for the bl2seq tool, but I didnt find it. After some research I found that bl2seq is only found in the legacy blast package. So my question is...
View Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
View ArticleBLAST: Querying a single sequence without input file in C
This is with reference to the query posted in https://www.biostars.org/p/17265/. If I try to run the following using command line it runs perfectly fine: blastn -query <(echo -e...
View ArticleHow To Automatically Screen Thousands Of Sequences Using Vecscreen
I looked at the NCBI Vecscreen website (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html), and you can put multiple sequences in fasta format in at a time. It allows you to download results, but...
View ArticleBlastclust Output Problem.
HI,I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file...
View ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View ArticleHow update Blast+?
how i can update Blast+?, because i have the 2.28 version, and i wanna update to 2.29 version, but i dont know if i need to download and install, or i need to unistall the previous version, or if exist...
View ArticleAffine gap penalty in Megablast
Dear all,I have a question. In megablast I don't understand why the existence and extension gap penalties in affine model are in that way. I thought the existence gap score must be always larger than...
View ArticleAlternative To Local Blastplus To Blast 10000'S Sequences On Nr, Swissprot...
Hi,Here is a case scenario that happens quite often to me: I need to blast from 1,000 to 20,000 sequences in order to find the proteins these sequences code for. These sequences come from fish cDNA...
View ArticleAlignment Matrix
Dear all,I have a problem with the following website:http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096More specific, I have a problem with the matrix (completely...
View ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
View ArticleComparable E-Value Among Blast Programs
If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be...
View ArticleAre old versions of NCBI's nr stored somewhere?
Hello,I'd like to study how NCBI's non-redundant protein database (nr) has developed over the years. However, I'm yet to find a way to download anything but the latest release from the NCBI ftp. Are...
View ArticleBlast Database Size Influence On Number Of Significant Hits
I have a set of gene sequences and specific sequence.cat genes.fa>Gene_1_chr1_1000_1200 ACGT...>Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search for...
View Articlencbi-blast warning: Selenocysteine (U) at position ** replaced by X
Hi all, I just want to know what does this warning message means.There's a way to suppress blast+ warings? The old blast has a flag -warnings as parameter, but the blast+ doesn't.
View ArticleAlternative to blast, faster but less sensitive?
I am looking for an alternative to blast that can search the UniProt sequence database in a faster way by losing some sensitivity. I am interesting in finding only relatively close homolog sequences,...
View Article