Any 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 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 ArticleHow To Get Blast+ (Stand Alone Blast) Output To Contain Only The First Hit...
Greetings! I'm using BLAST+ v. 2.2.26, and would like to customize the output to include only the FIRST hit for each separate record in the data base. The region I am using as the query is a domain...
View ArticleBlast+ Query Splitting/Chopping In Blastxml Format
What's the easiest way to split a BLAST+ query into pieces BLAST+ all of the chunks with blastn against NT, and merge them back together? I presume using query_loc is better than literally splitting...
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
View ArticleBest Hits From Blast Tabular Output Of Multiple-Queries
Hello. I have been trying to get the best hits out of blast output files. I know that -v option or maxtargetseqs in standalone blast gives the best ones. But I already have a huge output of multiple...
View ArticleHow To Extract Desire Genes Blast Xml Result From A Big Blast Xml File
Dear community, I have a XML file contained 50,000 genes Blast result with 10 hits for each gene. I want to mine desire genes Blast result from that XML file and the output file is still in XML format....
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 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 ArticleShortlisting Genes From Various Gene Prediction Methods Based On Blast Results.
Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
View ArticleLocal 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 Articleshort protein BLAST
Dear AllI am performing BLAST. The database is a collection of short protein sequences (~40 aa in length, short but not short very much). The query file contains short protein sequences as well (~40...
View ArticleStrategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View ArticleAre Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or...
Very simply, what are the units of the alignment length reported by BLASTX and BLASTP? The units of length are not listed in the output column headings (-outfmt 7) and I have found nothing in the...
View ArticleTaxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
View ArticleConvert Blast Table With Hsps To Alignment
HelloI have the following BLAST table format output:GRMZM2G5555 GRMZM2G5555 100.00 5197 0 0 2886 8082 2886 8082 0.0 9880 GRMZM2G5555 GRMZM2G5555 100.00 1418 0 0 1 1418 1 1418 0.0 2769 GRMZM2G5555...
View ArticleHow To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
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...
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