Blast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleWhy does Blast report a different alignment when using the -m8 option
i really need to know why when i do a blast with the option -m8, i have different results (different % identities, and gaps). example..normal >tr|Q3T560|Q3T560_9GAMM Arsenite transporter ATPase-like...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleCustomize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
View ArticleHow To Scale A Pssm For Ncbi Blast
Hi again,I'm trying to do a local NCBI BLAST search using the PSSM of a conserved CDD domain (.smp file in the database, cave LARGE file).My database is containing nucleotide sequences and the PSSM is...
View ArticleComparing Genome Derived And Cdna Derived Protein Sequences
I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.One of the protein sets is derived from comparing the genome with all the proteins of a...
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 ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View ArticleHow to identify transposons in a non-model organism transcriptome
I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them....
View ArticleAssemble Before Blast Or Blast Before Assemble?
Dear all, I posted a similar topic recently. I have a few draft genome data, all of which contain roughly 12 million 88 bp reads. I also have ~200 genes from reference organism, and need to find...
View ArticleProtein Sequence Alignment Using Blast
Hi All, I am trying to run Blast over protein sequences from two organisms. I downloaded the fasta from NCBI. I am trying to iterate over the list of sequences in the fasta file and do a sequence...
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 ArticleAfter Clustal analysis and MEGA analysis how can I obtain the probable...
I did my blast search with protein sequence of interest and then aligned it using Clustal w, did phylogeny analysis using MEGA 6. Now how can I obtain the amino acid sequence of a probable ancestor of...
View ArticleFilter command-line BLAST results by organism
In legacy blast (blastall) it was easy to do a remote BLAST query from the command line that only returned hits for a single organism: blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i...
View ArticleExtract Specific Entries From Blastx Output File, Write To New File
Hello, I have created a script that successfully searches for keywords (specified by user) within a Blastx output file in XML format. Now, I need to write those records (query, hit, score, evalue, etc)...
View ArticleGetting Taxonomy Lineage From Ncbi Gi Or Accession Number
Hey GuysI have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not...
View ArticleAnnotating sequences after de-novo Trinity assembly and RSEM analysis...there...
Hello, I'm hoping someone can provide some insight or point me in the right direction... I have very little programming knowledge and am fairly new to RNA-seq but I'm sure there must be an easier way...
View ArticleHelp! I Can Successfully Run A Blastp Search In Bioperl But I Want To Also...
I am new to Perl/Bioperl and have run into a problem. How can I perform a blastn search on a DNA sequence? I can successfully perform a BLASTP search, but I can't find any documentation in cpan or...
View ArticleHow Reproducible Are The Results Programs Compiled With Blast Libs Vs Calling...
Is there a risk that using the blast libs to do blast work could result in reproducibility issues if someone were to spot check the results with the NCBI executable? I am working on a program to do...
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