How Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View ArticleBlast2Go Save While Working
Hi I am running blast2go for a huge set of sequences. I would like to save the blast results from time to time (in case there is some problem with the computer, not to begin everything from the...
View ArticleFind Genome Source From A Blast.
Hi, I've made a blast with the sequences from a plant's transcriptome which don't match to our genome. We want to know where they come from to try to improve our genome. The problem is that I have...
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 ArticleIdentify short repeats in DNA sequence?
I want to identify the short repeated sequences in a given DNA sequence. For example, the sequence I have is atacctgcc ccc atacctgcc. The repeated sequence is 'atacctgcc'. Is there a program to...
View ArticleCompare Two Sequence To Find The Maximum Similarity
We know BLAST can compare two sequences, however it compares sequences by lining up them. My question is can we shift one sequence then compare the other. Let me give you a simple example:the length is...
View ArticleNCBI GI to Gene Description
Hello all,I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed...
View ArticleBlast Output Into Jsp/Html
I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?
View ArticleHow To Concatenate/Merge Blast Xml Outputs?
I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates...
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 ArticleComparing Bowtie H_Sapiens_Asm Blastn -Task Blastn-Short -Db Human_Genomic
I am thinking the current supplied (pre-formatted) blastn humangenomic database from NCBI contains many many duplications of the same sequences. Is this correct? I think I only need the current...
View ArticleWhat are the "Coding", "Maximal" and "Two templates" options for megablast?
"discontiguous megablast" on the NCBI website, as well as other implementations, appears to have a "Discontiguous Word Options" parameter set. These include a template length and template type; the...
View ArticleRemote blast+ skipping query sequences
Hi, I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:time blastx -db nr -query...
View ArticleGiven Sequences, How To Compute A Low Complexity Score For Each Sequence?
Is there a way or a program/module that I can use to compute the complexity score for the given sequences? I want to rank sequences by their complexity.
View ArticleGene Ontology Tool Selection
I am trying to do the gene ontology analysis based on the gene duplication to see weather there are any difference between gene duplication genes and control. I used the BLAST2GO a lot to get some...
View ArticleAfter Clustal analysis and MEGA analysis how can I obtain the probable...
I did my blast search with protein sequence of interest and then aligned it using Clustal w, did phylogeny analysis using MEGA 6. Now how can I obtain the amino acid sequence of a probable ancestor of...
View ArticleWhat Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To...
I have to perform 'fragment recruitment' on my metagenomic reads to generate plots of the percentage identity in the reference sequences. From what I can tell, fragment recruitment just amounts to...
View ArticleProblems running local Blastp: No hits found when there should be
Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results. blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml -outfmt 5 -query...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleFinding an exactly conserved amino acid sequence in a particular protein.
Hi I've been trying to find a perfectly conserved region of a particular protein (secY : a membrane translocase ) among all species of Leptospira. I tried using microbial BLAST, but this isn't very...
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