Can You Explain The Differences Among These Blast Databases?
I am trying to blast my sequence against primate databases remotely. But there are so many databases, and most are in abbreviation. Can you explain what they are in the below example list? chimp AACZ...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleMakeblastdb Error In Blast+ 2.2.26
I am running makeblastdb from blast+ version 2.2.26 on uniprot_trmbl.fasta and get the following errorBLAST Database creation error: Error: Duplicate seq ids are found: GNL|BLORDID|2707210Any ideas...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleThe Meaning Of The E In Blast Output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
View Article[Help]: Extracting Sequence From Fasta Using Blast Informations?
Hi there! This is my first post on your forum and I hope you'll be able to help me. This is my first intership in bioinformatics and I'm kind of learning everything by myself. I learnt how to use...
View ArticleBlast2Go Doesn'T Work With My Fasta File
Hi all, i downloaded human unigene fasta file from Here (Hs.seq.uniq.gz with .uniqe format), and change it to .fasta by notepad. when i submitted the file to blast2go it doesn't work and give me an...
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 ArticleBlastdbcmd Cant Find Protein Database
Here is the command I used:blastdbcmd -entry_batch input.gi.txt -out file.out -target_only -outfmt %t -db my_protein_database.fastaI got an error "Error: Entry not found in BLAST database". I have the...
View ArticleWhy am I getting the BLAST option error: file does not match input format type
COMMAND USED: makeblastdb -in sorted_alu_seq.fasta -dbtype 'nucl' -out aluBLAST option error: sorted_alu_seq.fasta does not match input format type, default input type is...
View Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View ArticleHow Can I Sort Blast Output Based On E-Value?
Hello: I have a blast output with about 50000 sequence list. The problem I have is that I need to sort those results based on the smallest e-value to greater e-value. Could you guys please suggest me...
View ArticleBlast To Cytoscape
Hi Guys, I am trying to view the results of an all vs all blastp of some sequences with cytoscape. I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a...
View Articlerps blast database 'formatrpsdb' problem
Hi.. After installing BLAST+ package from ncbi, when i try to build a database for rps blast analysis using: formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0 it gives following error:...
View ArticleHow to analyze the ProDom output? I have some results to support the...
Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View Articleblasting genome contigs against local SILVA 16S RNA database
Hi All,I'm new to bioinformatics and interested in determining the bacteria strains in a collection of bacteria genome contigs. I wonder if is logical and appropriate to create a local SILVA 16S RNA...
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 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 ArticleLocal Blast Returns No Result, While Using The Website There Are Some Matches
I want to blast some EST with local blast. However, for some sequences, there are no matches while with the website http://www.arabidopsis.org/Blast/index.jsp.(I download the database from the site,...
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