Primer design using Bioinformatics tools.
Hi, I am currently working on a project designing a primer template for detecting any pathogenic species of leptospira in a serum sample, but I seem to have hit a roadblock. While the ncbi primer...
View ArticleLocal Mirror Of Biological Databases
I'd like to set up a local mirror of certain large databases like the nt BLAST database, interpro etc.The biomirror project looks like a good candidate, but they seem to advocate using GridFTP, and...
View ArticleReciprocal blast and protein identification
Hi Guys,I am doing reciprocal BLAST to identify members of a protein family in different species. Is it necessary for me to set a strict e-value threshold while doing each BLAST? What I am doing is I...
View ArticleClik here to view.
How Do I Interpret Ebi Blast'S Visual Output?
Following is the visual output for EBI's blast service. I don't understand it completely. I get that the left side is my sequence and right side is the subject sequence. What exactly are the colored...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleOrthomcl Blast Error: No Hits Are Being Saved
when i try to run blast in orthomcl using the command below:blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes -soft_masking true...
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 ArticleError While Running Standalone Blast Via Bioperl
Dear All,I am trying to run a stand alone blast in my system. I have created a database locally and I am tying to run the blast against them using STANDALONEBLAST module of bioperl. The code is as...
View ArticleConvert Blast m8 output to XML
I've used usearch's ublast feature on my datasets. I'm now wanting to use a package such as findorf on them. However, this requires XML formatted data, which usearch does not support as output. I have...
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 ArticleVertebrate Subset Nr Database? Build My Own?
I think I have the answer to my own question, but I'm somewhat new to bioinformatics, and I want to make sure my strategy is sound (and that there are no easier solutions to my problem). We need to...
View ArticleMerging Blastx Hits From Overlapping Bacterial Genome Segments
I blastx-ed 1Mbp bacterial genome fragment against NCBI nr database. I have split it into 2000bp fragments with 500bp overlap into a one multiple fasta file (splitter from EMBOSS) splitter -sequence...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
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 ArticlePython/Perl Script For Defining Minimum Coverage Of Blast Match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View ArticleBlast+ Error
hi，everyone！ I use blast+ to make annotation of RNA-seq data against nr. When I run blast, it always stopped by error. my command line is "blastn -task blastn -query Unigene.fa -db human.rna.fna -out...
View ArticleProcess tabular BLAST output
Dear all,Iam struggling with processing tabular BLAST output. I would like to do the following:Take a Blast output table (simplified):Sequence ID | e-value | GISeq1 0.001 12345Seq1 0.001...
View ArticleRetrieving Results Using Blast Soap Api
Hi ; I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:"blasp.exe -query input.txt -db...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
View ArticleBlast Results Wont Return
This isnt my usual way if doing things but because im using Plone it has to be done this way. The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able...
View Article