BLASTP 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 ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleStrategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
View Articleshort protein BLAST
Dear AllI am performing BLAST. The database is a collection of short protein sequences (~40 aa in length, short but not short very much). The query file contains short protein sequences as well (~40...
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 ArticleFinding mutations conferring antibiotic resistance
Hi All, What bioinformatics approches can I employ to determine antibiotic resistance in bacteria strains conferred by the 23S rRNA mutation, or any other gene generally speaking? Thanks
View ArticleIdentification Of Promoters From Gene Sequences And A Vertebrate Genome Assembly
I have a number of genes which I'd like to locate in a whole-genome assembly, in order to identify the genes' promoters. In the past I've done this manually using BLAST and BLAT, which has worked well,...
View ArticleFASTA-Reader: First data line in seq is about 100% ambiguous nucleotides...
I am not sure if this is a problem or if in fact the process is correct. Any help is much appreciated. I am trying to make blast databases from assembly fasta files, and have seeing the above error. It...
View ArticleRefseq proteins for several taxids
Hi all,My question may sound simple. I'm trying to download the plant ref-seq proteins from NCBI to make blast database and run blastx for contigs resulted from de novo assembly of a non-model plant....
View ArticleWhere can I find human protein database to download for blastx?
Where can I find human protein data base for local blastx? I have already blasted my transcriptome against the nr database. My adviser wants me to blast it against the human protein database and find...
View ArticleHelp mapping NCBI BLAST output to Biomart
Hi Everyone,Does anyone know know what attributes I can map the NCBI Locus, Accession, or GI to using Biomart in R? I've tried everything without any luck, including EMBL (which the Biomart meta says...
View Articlepredict binding affinity
Hi all, If I know amino acid sequence or nucleotide sequence of a ligand and that of a receptor, can I predict the binding affinity between the ligand and the receptor? What is the state-of-art program...
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 ArticleBest Hits From Blast Tabular Output Of Multiple-Queries
Hello. I have been trying to get the best hits out of blast output files. I know that -v option or maxtargetseqs in standalone blast gives the best ones. But I already have a huge output of multiple...
View ArticleBlast2Go Statistics
HI When I run blast2go I want to receive statistics about how many sequences fit to each category. When I go to statistics in the blast2go I only manage to generate graphs. How can I receive the data...
View ArticleHow To Find Sequences With A Given Number Of Mismatches
Hi! Is there any script or tool that allows to find similar sequences given the maximum acceptable number of mismatches? What I want is something similar to a Blastn search, but instead of filtering...
View ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleMakblastdb And Low Complexity Regions
Hi i want to create a blast database from sequences that under blast are marked as "low complexity", is there a way to make makeblastdb turn off this filtering?i'm aware that the sequences might be...
View ArticleWhat Is Score Bits In Blast?
i want to konw that what does it mean score and bits in local blast output from the following example?'. Score = 38.2 bits (19), Expect = 0.11 Identities = 22/23 (95%) Query: 1 cttaacttcagctacctcgagta...
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