Ways To Quantify Proteome Analysis Via Blast
I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database....
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 ArticleFind All Similar Sequences In Genbank
Hi, I would like to get a feel for how many sequences related to my virus of interest are available on GenBank. I am thinking about using a recursive BLAST approach. Start with one genome, BLASTn, and...
View ArticleStrategizing Blast Result Parsing
I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you can imagine, my blast results for this dataset are redundant in the...
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleFormatdb From A Batch Of Fasta Sequences
Hi I have a batch of fasta files, each one is a file of ESTs from a different plant. I want to create a database for all the plants, how can I use formatdb (or another way) to create one database which...
View ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
View ArticleClik here to view.
Tool: Automatically download NCBI Blast databases
HiI thought to share this tool, in case you need it. The tool automatically downloads ALL NCBI blast databases from NCBI ftp server. Limitations:You can stop a download and resume later as long as you...
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 ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View ArticleIs A "Gene-Like," Returned By Ncbi Blast, Indicative Of Gene Family Membership?
I'm looking to sequence HSD in a non-model organism. I've been using degenerate primers for awhile and finally got a successful sequence. BUT when I enter it into BLAST, I get high sequence identity...
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 To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View ArticleRunning Blast With C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
View ArticleQuestion Regarding Blast And Blat Function
The attached file mouseReads.fasta (Copy/pasted below) contains 67 short reads from a mouse RNA-Seq experiment. The reads were downloaded from the NCBI Short Read Archive. Millions of reads were...
View ArticleHow Can I Determine Whether Two Proteins Have The Same Multi Domain...
How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of...
View ArticleBlast A Specific Contig Against Multiple Contigs From Another Organism
I have a contig from one organism that is of interest. I have been searching this contig against another organisms complete collection of contigs found on NCBI by using an online DNA translator and...
View ArticleMachine Spec For Running A Blast Service For ~50 Users
I have been asked this question by a friend, but I didn't feel I could give a satisfactory answer. Maybe somene here at BioStar can share some experience.The question is: what kind of hardware would...
View ArticleScientific Notation In Blast
Hi there,I've to choose some sequences from blast result which are under 10^-5 Results are in scientific notation. How can I convert scientific notation to double? Which is the double for 2e-104 ?Thank...
View Article