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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Facing problem with BLASTx using BioPython in Google Colab
I'm trying to BLASTX a sequence using Biopython in Google Colab. Here is the code I am using. I'm not able to understand why I am getting an empty list [] for ...
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I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its ...
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Binning then assembling sequencing reads
I am attempting to do something similar to the "Phylomapping" pipeline described in this paper: https://www.nature.com/articles/s41559-019-0914-2. I have sets of Illumina PE reads, that I ...
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BLAST Database error: No alias or index file found for nucleotide database
I have created a database and added environment variables, but an "error message" still appears. How can I solve it?
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How can I Find DNA sequence of promoter region of a gene?
I have a fungal sequence from Candida albicans, sequenced via Sanger sequencing, that I want to check for quality and contamination.
I have 2 questions:
Could I use Alignment ? or BLAST or ...
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How do I identify gene duplication or paralogs in an annotated reference genome assembly
I generated a high quality de novo genome assembly which has been annotated using previously published isoseq data from the species. This genome is now the Refseq for the species. I am currently ...
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Need to find an intersect of sequences inside fasta files (no standardized sequence names)
I have several multifasta files (each containing between 3,000 to 3,600 sequences). The sequence names were derived from the genome where the sequence was extracted and they bear no significance or ...
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What does this BLASTN mean: Error pre-fetching sequence data?
I am trying to run BLASTN on a 14GB Pseudomonas database using the command: blastn -db ~/pseudomonas-db/pseudomonas -query ~/desktop/inputfiles/poz176.fasta -out poz176-out -num_threads 8
I get the ...
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How can I limit blast results to exclude a specific taxonomic ID?
I would like to perform blast+, using the command line, here is the code:
-task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote.
I have to ...
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Blastn through NCBIWWW not giving any results, as opposed to the online BLAST
I am trying to create a simple pipeline that takes a file containing various short sequences, and run them through blast. I have an example sequence;
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retrieving past BLAST requests in bioPython
is there any way to retrieve a BLAST request made using the Biopython library using the request's query_id?
Alternatively is it possible to retrieve a query_id before the blast result is complete, and ...
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how to use BLAST+ in an optimal way
I have a 32-bp query that I want to perform BLAST+. my query represents different RNA viruses and I do expect that my hits get more than 500,000.
but in practice, when I perform it I get around only ...
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How to BLAST a protein against a large set of organisms?
I have a list of organisms with their full scientific names and Taxonomy IDs, total ~1500. I want to BLAST my protein against this 1500 genome or proteome. How can I do that?
Here a sample protein ...
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BLAST+ not working on my Command Line
As you know, ncbi has several databases, including nt, nr, etc.
What I am going to do is to blast a sequence of approximately 30 base pairs to the nr database and extract all similar sequences.
For ...
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Parameter optimisation of minimap2
I'm leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files.
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M__♦
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