Extract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
View ArticleNeed a help re Blastn against short (~50 nt seq)
Hi Evevryone,In stand-alone blast, I'm blasting several thousands of ~450nt long sequences against one short ~50nt long motif sequence to find the sequences that has this ~50nt motif. In blastn output...
View Articlephylogeny tree after a blastx run
Hi!I just run a blastx , using a nucleotide sequence and 192 Blast Hits returned. What i want to do is to create a phylogeny tree to see which organism from blast's results are closer genetically to my...
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 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 ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View ArticleDatabase Error When Running Blastn
Hello, as initially stated here, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.What I get is:BLAST Database error: No alias or index...
View ArticleBlast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Hi all!I am running blast 2.25+ and willing to get output in format 7, setting -outfmt 7. However, with this setting I always get Segmentation fault. Same happens with -outfmt 6 and 10. Other settings...
View ArticleComparing Genome Derived And Cdna Derived Protein Sequences
I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.One of the protein sets is derived from comparing the genome with all the proteins of a...
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
View ArticleWhat to use for a measure of distance between two sequences?
I've got a lot of genetic sequences and I'd like to use various clustering algorithms on them, but this requires a measure of the distance between two sequences. I've used BLAST+ and the...
View ArticleGet Query Coverage From Local Blast
Hi allDoes anyone have an idea how I can get the query coverage of my hits from local BLAST (in unix). The -m 8 option gives you a tabular output that does not contain the 'Descriptions' part of the...
View ArticleBlastx For A Million Metagenomic Sequences
I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my...
View ArticleBlast Settings For Short Sequences
I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:>ponzr CGCGGTAAAACACATTTG And...
View ArticleAre There Local Aligner Like Blast Working On Unicode Characters?
I want to use a blast-like local aligner to find common substring between common human readible texts. e.g. social media data. A normal plagiarism finder won't do because the intention is to align GB...
View ArticleBash Script To Filter Blast Xml Output
I have read the instruction here:XSLT stylesheet to filter blast xml output And here:How to filter a blast xml output ? and I came up with this script:#!/bin/sh # # filterblastxml.sh : Script to filter...
View ArticleImport Xml Blastx Results In Geneious
Hi,I have the xml results file of my local blastx and I would like to import the annotations directly on my sequence in geneious. Do you know if there is a way ?Thanks,Aurelien
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleIs Matching Blastn Output A Requirement For Alternative Sequence Matching...
I've read a paper demonstrating an implementation of sequence alignment and the authors indicate that in order to provide substantial speed gains they must compromise on query size and output fidelity,...
View Articleblast output for FASTA (aligned sequences) to get organism name
Hi,I want to get the organism name from blast output (FASTA (aligned sequences)) for the specific protein.I am a beginner in python. Please help me to write the script for getting organism name in...
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