How To Filter A Blast Xml Output ?
Hello list, I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a...
View ArticleHow to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View ArticleLocal Fasta Query Using List Of Gi Accessions
Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.
View ArticleAny 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 ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleBlast With Amazon Ec2
Does anyone have any experience running BLAST with a local blast database on Cloud Bio-Linux through the Amazon EC2 infrastructure?I would love to hear how it turns out and is it worth the cost?
View ArticleConcatenating fasta files for BLAST
I have two fasta files from WormBase. One is the coding transcripts, the other is ncRNA. When I BLAST (using NCBI Blast+) 44k 60-mers against just the transcripts, I get 37,216 hits. When I...
View ArticleBLAST alignment score analysis
I've been evaluating a Smith Waterman implementation with ncbi BLAST and found out that for the same alignment (with no gaps) the alignment scores differ between those two algorithms. Here is the...
View ArticleSetting E-Value In Blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View ArticleRunning Blast On Amazon'S Elastic Mapreduce
Hello, I need to extract 10 million (yes, 10 million) sequences from the blast database -nt using the blastdbcmd command. Needless to say this will take days on my rinky-dink desktop ( In an earlier I...
View ArticleImport Xml Blastx Results In Geneious
Hi,I have the xml results file of my local blastx and I would like to import the annotations directly on my sequence in geneious. Do you know if there is a way ?Thanks,Aurelien
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 ArticleTool to map sequences and get genomic coordenates
Hello, Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the...
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
View ArticleOnline blast and standalone blast return different hits?
Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want 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 ArticleCommand blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
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 ArticleBlastp Against Human Proteome
Hey guys,I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans. I will run the...
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