Biojava And Blast+
Dear all, i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to carry out many blast searches from time to time, i decided to install the...
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 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 ArticleBlast Output With Species Name
Dear all,my question is very simple. I have reads from a human RNASeq and I would like to check for contamination on a specific virus family. So my pipeline looks like1) Align on the human genome...
View ArticleAlignment Matrix
Dear all,I have a problem with the following website:http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096More specific, I have a problem with the matrix (completely...
View ArticleBlast Gives Cryptic Errors
I have a list of proteins in fasta format (say goodProteins.fasta). I first make a compatible database using NCBI's formatdb v 2.2.18:formatdb -i goodProteins.fasta -p T -o TThis gives me a number of...
View ArticleHow To Extract Max Score Blast Hit Among A Data Set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
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Is the source code for the NCBI-BLAST service available anywhere?
Hello!Is the source code for the NCBI-BLAST service available anywhere? In particular, I'm interested in producing the visualization NCBI-BLAST offers, such as the one below, using BLAST results from...
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 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 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 ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View ArticleComparable E-Value Among Blast Programs
If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be...
View ArticleHow To Concatenate/Merge Blast Xml Outputs?
I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates...
View ArticleBlast Xml For Multiple Databases
Hello, I run blast2.2.25+ with multiple databases, I would like to view my result for each database in my XML result file, it is possible?
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 ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleBest Reciprocal BLAST and Alternative Transcripts
How sensitive is BLAST to detecting the various events that lead to isoforms of transcripts. I've had decent success in being able to capture orthologs things like nonsense mediated decay or highly...
View ArticleBlast Database Size Influence On Number Of Significant Hits
I have a set of gene sequences and specific sequence.cat genes.fa>Gene_1_chr1_1000_1200 ACGT...>Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search for...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
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