Local Blast Question About The Genome Download
Hello All,I have trying to go local blast for my genes (55 in number). I need to find the genes in all the mammalia class. I was trying to download the genomes for all the species of interest but I...
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 ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleQuality Analysis Of Pacbio Data
Hey GuysJust wondering if you guys have come across or developed any process to check for contamination in PacBio reads. By contamination what I mean is to align/blast the PacBio reads to some...
View ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
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 Articleproblem running local blast after downloading on MacOSX
Am newish to linux but very familiar with BLAST and I need to use BLAST locally through command line on my MacOSX (Yosemite)I downloaded the BLAST+ using ncbi-blast-2.2.18+.dmg installer and following...
View ArticleFunctional Annottations From Blast.
Hello, I'm writing a program that takes sequences in some format (FASTA for example) performs a BLAST search on it and takes a funcional annotation of each result, then looks in Gene Ontology database...
View ArticleCreate a custom .gtf file with a list of genes
Hi GuysI am new to the RNA Seq world and just starting out with linux. I need to create a custom gene annotation file with a list of genes I am interested in analyzing. How do I do that.
View ArticleUse Megan To Parse Sam File
Dear all, I got a question about using MEGAN4 to parsing SAM file. What I want to do is to get taxonomic and functional annotaion of my raw reads against nr database . As the raw reads is too big (11...
View ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
View ArticleWays 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 ArticleProblem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
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 ArticleBlast: Homology Or Similarity?
Hi Biostars, I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search? thanks EDIT The BLAST is performed against a custom DB containing only homologous proteins.
View ArticleHow To Build The Correct Blast Url For The Rest Interface
Hi All,I am having difficulties constructing a BLAST query via the REST interface. In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences. The URL I...
View ArticleHow to Delete Hits from an original sequence
Hello,Using standalone Blast, I used BlastP to align the human proteome against a bacterial proteome, this gave me a number of hits where the human proteome has been found within the bacterial...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the...
View ArticleDefine Blast Xml Parser By Dtd
I have seen many examples of using a DTD to validate XML documents, but I was wondering if they could be used to dynamically define a document at runtime. Specifically, I was wondering if a DTD and a...
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...
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