Determining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleBlast Output With Species Name
Dear all,my question is very simple. I have reads from a human RNASeq and I would like to check for contamination on a specific virus family. So my pipeline looks like1) Align on the human genome...
View ArticleParse Blastdb Format From Java
Does anyone know a java library to parse blastDB files? I've found the specification at http://selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html for the file format, and the code for a C...
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 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 ArticleOpening A Fasta File In Windows
Hi all,I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format and then format it using makeblastdb.then extract the first 1000 characters...
View ArticleCan Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline...
Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by putting the stdout from the wrapper into a python string variable and then using NCBIXML.parse to parse...
View ArticleHow To Blast A Fasta File That Is Non-16S
Hello,I have a Illumnia generated fasta file that was created using rpoB sequence data. I am looking to BLAST these sequences in order to find the best 3 hits of what organism I am looking at. I know...
View ArticleBlast Against Pdb Standalone Version
HiI have always used the online service of pBlast and now I am a bit confused since I want to use its standalone version. My aim is to blast a protein fasta sequence against PDB and save all the pdb...
View ArticleCommand Line Blastplus Strange Results
I am running command line blastn with a local copy of a microbial database. My command looks like blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2 -gapopen...
View ArticleScript Or Tools To Blast Primer Sequences Against Fasta File
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View ArticleBlast Database For Bos Taurus
Hello To All,I want to blast my sequence Only in Bos taurus database Using local Blast (Blast+). But I don't know which database I should use for this from this...
View ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleHow To Make Statistics Of Mismatch And Unpairing Positions Between Mirnas And...
Dear all, i need to make statistics of mismatch and unpaired positions between miRNAs and their targets. What I have done is that I performed patscan and identified miRNA targets using various patterns...
View ArticleHow To Downlad Blastall Executable
Hi,It seems that the old version of blast (blastall) can make use of multithread processing and speed up things whereas new blast+ versions get stuck to using single thread even when you set the...
View ArticleThe Meaning Of The E In Blast Output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
View ArticleWhich Bioperl Module Can I Use For Parsing/Mining Blast Output?
Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in...
View ArticleHow to perform phylogeny analyses
i want to do project on phylogenetics on hiv subtype-1.but how i start the project on this ,what tools are apply on this.
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