Questions tagged [blast]

Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.

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1answer
1k views

Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

Disclaimer: This is a self answered question for documentation purpose and I adapted this from the following github gist. Especially from users terrycojones and peterjc as well as sujaikumar who ...
3
votes
1answer
401 views

taxon exclude list for searching local blast database using blastn

I am looking for a solution to exlude certain entries when searching a local blast nt database (with blastn), specifically the sequences from uncultured / environmental samples, ideally using their ...
4
votes
3answers
324 views

Finding orthologues using BLAST on the NCBI database

I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?
2
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1answer
278 views

Merging / Concatentating BLAST Databases

I was wondering if any one has had success merging BLAST databases from multiple references? For a concrete example I have hg19 and a bunch of viral and bacterial genomes that all have been index ...
6
votes
1answer
372 views

Blast hits disappearing after changing -evalue

I was teaching an introduction to bioinformatics when the students and I noticed strange Blast behavior that we couldn't explain. With the default evalue parameter,...
4
votes
1answer
1k views

Calculating bit score: How do you find lambda and K?

To calculate bitscore from score you can use this equation: $S' = (lambda*S - ln(K)) / ln(2)$ If I am trying to manually calculate the bitscore of an HSP of a pairwise blastn alignment, and I know ...
1
vote
1answer
50 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
1
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4answers
312 views

How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms

I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly. I analyzed both isoform and gene expression abundances using RSEM....