Blast Result Matching Both Of Two Query Sequences?
If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity...
View ArticleAssemble Before Blast Or Blast Before Assemble?
Dear all, I posted a similar topic recently. I have a few draft genome data, all of which contain roughly 12 million 88 bp reads. I also have ~200 genes from reference organism, and need to find...
View ArticleLocal Graphic View Of Blast Results
When I do local BLAST with the parameter -m 8, I find that one query sequence can match the same subject sequence at several parts. I wonder if there is some tool that can read the BLAST m8 output and...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
View ArticleOutput blast and time execution
Hi,I have a simple question. Why the xml output format in blastn take a lot longer than the tabular output ?There is a huge difference between the two output formats, using the same data and...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleAbout Blast Scores In Matrix Format.
Hi All, How Can I get local Blast score in matrix format??( I have score but I need in Matrix format) How can I run blast of 200 sequences in order to alignment sequences by writing a python...
View ArticleHow To Remove All Sequences In My Custom Blast Database?
Is it possible to clear a blast database once you have made it? I mean I created my custom database with nucleotide sequences, but I think I messed up something so I need to empty/clear my database and...
View ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
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...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
View ArticleProblem In Making Blast Database (Makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
View ArticleObtaining the top matches from blast
Hi,I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have....
View ArticleIdentifying closest homologue of a protein sequence
HI, I have this list of proteins from a new genome project so its pretty much unannotated. However, its closely related to C. elegans so i was thinking of trying to identify the closest C. elegans...
View ArticleNgs 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 ArticleMultiple Psi-Blast Iterations From Command Line Using Remote Database
When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working...
View ArticleBest Practices/Methods For Developing Bioinformatics Related Web Applications
Hello everybody!I'm planning to transform a few windows programs which I wrote into web applications. Can anybody give me some tips, suggestion or experience with this (Framework, Hosting)? I will use...
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleBLAST database files
After I run makeblastdb against a fasta file, I get nhr, nin, nog, nsd, nsi and nsq files.Questions1) What do these file extensions mean?2) Do these files replace the original chrY.fa file which was...
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