" ERROR: ObjMgrNextAvailEntityID failed with idx 2048" when using blastpgp
I am running blastpgp using as query a .faa file containing around 31.000 seq. My db contains also more than 50000 seq, and I select -m 9 to have a tab del output. During the run I get the following...
View ArticleFinding Lincrna Alignments With Blast Versus Blat
Hello,I have a lincRNA sequence (XLOC) that I retrieved from the Broad Institute. When I BLAT the sequence against the human genome, I get a 100% match and it aligns with the correlating transcript...
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 ArticleBlast Is Giving Me A Result Totally Unrelated To The Gene I Expect
Hello,After I obtained the results from sequencing, I proceeded to curate the sequences and identifying (with Vector NTI) the primers I used in the sequence. The primers, although are degenerated, were...
View Articleclustal w result interpretation
I used microrna in clustal w software to remove redundancy . some part of output was like this ..can any one tell how to interpret the results ..... what is that score. how can i know wether the...
View ArticleBlast Against Swissprot Db
Hi I downloaded the swissprot database and used the command formatdb and then tried blastx against this database, I used the command: megablast -b 1 -T T -i....results.html I received results but with...
View ArticlemiRNA -identification animal
Currently I am predicting miRNA in animal.. when I perform BLASTx, i dont know how to select the non-coding protein? plz help me.. Do we have any other softwares or tools to remove coding protein??
View ArticleLooking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
Hi allI am building a pipeline for taxonomically identifying a blast result at each taxa level, with a bespoke reference dataset. I want it to be easily reproduceable, which it is, other than an ugly...
View ArticleFunctional Annottations From Blast.
Hello, I'm writing a program that takes sequences in some format (FASTA for example) performs a BLAST search on it and takes a funcional annotation of each result, then looks in Gene Ontology database...
View ArticleRunning A Standalone Batch Blast With Fasta File Using Perl, Can'T Get...
I'm running standalone blast locally. My blast query sequencess are in a fasta file called human_seqs.fasta, which comprise around 300 sequences. Being blasted against a much larger database called...
View ArticleFinding The Gene Annotation Output From Web Blast In The Xml Etc. ?
Hi, I'm new to bioinformatics and am still learning how all the public databases interconnect so please bear with me :) I have de novo assembled a set of bacterial genomes, located and extracted...
View ArticleGene Function through sequence homology
HiSo I've got list of genes putatively involved in Leptospira virulence, and I want to produce hypotheses on their function through sequence homology. So I was thinking of BLASTing them as a first...
View Article/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....
Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the...
View ArticleBlast2Go Graphs
I perform blast in the blast2 go and then the GO and annotation steps. In previous projects I had the option to create "direct Go count" graphs on the process, function and component. I remember that...
View ArticleHow Ncbi Blastn Gets The List Of Organisms Programatically
Hi, Those who use the NCBI BLAST web site recognize the "Choose Search Set" box. After you select OTHER database and you type - in the Organism edit field - an organism name, similar organism names are...
View ArticleBlastall gives several hits to the same subject sequence
Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best...
View ArticleMakeblastdb And Blastx
Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with...
View ArticleHow To Get Status Update In Ncbi Standalone Blast?
For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any...
View ArticleStrange "Error: OID not found" in NCBI's blastdbcmd
I'm getting a OID not found when executin blastdbcmd. My file is as follows:>cat data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted | grep scaffold00001_37_1_21>scaffold00001_37_1_21 And...
View ArticleBl2Seq With Multi Fasta
Hello,I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot runbl2seq -i 1.fa -j 2.fa -p blastp -o outputbecause bl2seq is...
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