Low Stringency Blast (To Find Outgroups)
Hi!I'm looking for a way to find appropriate outgroup sequences for my paralog phylogenetic tree. Is there a way, using blast, that I can find sequences that are only a little similar to my query...
View ArticleMakeblastdb Error
I ran into the following error when trying to build a database using makeblastdb (NCBI BLAST 2.2.23+).> makeblastdb -in uniprot90.faa -dbtype prot -parse_seqids Building a new DB, current time:...
View ArticleHow Reproducible Are The Results Programs Compiled With Blast Libs Vs Calling...
Is there a risk that using the blast libs to do blast work could result in reproducibility issues if someone were to spot check the results with the NCBI executable? I am working on a program to do...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
View ArticleTutorial: Installing And Running Ncbi Blast
##rest "Installing and Running NCBI BLAST" tutorial imported from the MSU course Analyzing Next Generation Sequencing Data (http://bioinformatics.msu.edu/ngs-summer-course-2011) You should start this...
View ArticleForum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
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 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 ArticleExtracting Fasta Alignments From Parsed Blastxml File
Hello, I have cobbled together a small script that parses a BLASTxml file. It seems to parse the xml file just fine (judging from what it prints to the screen). The problem is the hsp.fas alignment...
View ArticleBlast Fatal Error -Database Not Found
I am using blastall 2.2.26 on ubuntu for local databse blast forQuery: c4_n2_train.fasta;Database: c4_n2_test.fasta;With my database files in the same directory, but still I am getting FATAL ERROR$ ls...
View ArticleIs Makeblastdb Creat 3 Files Like Formatdb + Blast Error
Hi everyone, I have a big problem!I install blast+ for windows.I run this :makeblastdb.exe -in filename.fasta -dbtype nucl -out filename_BLASTdbapparently it create db coz I have this message:a -dbtype...
View ArticleHow to use whole computer cluster power for computation of a single job?
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node , 80 cores) for a single job without breaking it. If I just submit it (a...
View ArticleAlmost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
I have pair-ended illumina samples with the read length of 100-150bp. I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie.When I blast them to nt...
View ArticleNcbi Web-Blast With Huge Subject Sequence Provided By The User In Fasta File
hello everyone,I tried to blast my query sequences with my subject sequences in fasta file...i uploaded both my query and subject sequences in fasta file to the ncbi blast page, but it didnot...
View ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
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 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 ArticleIn blastclust, is score density based on bit score or score?
I'm trying to understand the parameters for blastclust, specifically score density. Is this the raw score divided by the sequence length, or the bit score divided by the sequence length? The...
View ArticleHow To Run Genome Wide Local Blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
View ArticleWhat'S The Easiest Way To Blast 5000 Sequences Against An Exon Fragment?
I have 5000 EST sequences that I downloaded from Genbank. I have a 500 bp exon fragment that I'd like to BLAST against this lot of sequences to see if my exon is present or not. What's the easiest way...
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