Looking 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 ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
View ArticleHelp In Standaloneblast Bioperl
Hi, I am new to bioperl. I have been trying to run blast, I get my blast output, I am not sure, how to use $factory in bioperlI have blast installed and has been added to my PATH variable.use...
View ArticleDownload Ensembl Blastn Result
Hi,How can I download blast results from ensembl. I blast 10 sequences against all ensembl species. Now I have the result page and I want to download all hits to compare them.Is it possible ?Here's the...
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 ArticleProblem In Making Blast Database (Makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
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 ArticleTools For Validating Blast Result?
Hi Friends,After doing blast for my nucleotide sequence i have found out the homologous sequence based on the identity, sequence coverage and e value. Kindly tell me which tool will be best to find out...
View ArticleCommand Line Blastplus Strange Results
I am running command line blastn with a local copy of a microbial database. My command looks like blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2 -gapopen...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View ArticleUse Megan To Parse Sam File
Dear all, I got a question about using MEGAN4 to parsing SAM file. What I want to do is to get taxonomic and functional annotaion of my raw reads against nr database . As the raw reads is too big (11...
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 ArticleAssemble Reads According To Blast Result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleBest Way To Grab All Ncbi Protein Sequences For A Specific Taxonomic Query?
I would like to retrieve all of the NCBI protein sequences that belong to a specific taxonomic query, or children of that query. For example, I want to get every protein sequence belonging to the...
View Articlestart and stop position of mapping in Blast
I used makeblastdb to search many short fasta sequences in a known organism. I successfully completed this step and got the mappings. My question is1. how can I get the start and stop coordinate ?for...
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 ArticleWhy Default blast search result shows fractional scores at last?
I've runned Blast normally with default parameters. Alignment scores are give in fractions like 84.3. But the BLOSUM 62 matrix contains no fractional scores for any aminoacids..so I would like to know...
View ArticleKegg Mapping-What Does The Colour On The Pathway Means?
Hi all, I am doing transcriptome analysis and i have just performed GO-KEGG mapping with blast2go v2.4.2. The results contain maps with EC of multiple colour. Do any one know what all these colour...
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