3

1000 genomes, HGDP and SGDP all contain SNP data from individuals where the country of origin is known. They all have slightly different numbers of people from different populations (1000 genomes and HGDP have more individuals in each pop, but fewer pops, and SGDP is the opposite).


2

You don't want BLAST here, or at least not regular BLASTn. A better method would be to use tBLASTn to map the known C. Elegans proteins to the translated genome. However, I would recommend using a slightly more sophisticated approach: Collect fasta sequences of all known C. Elegans proteins (amino acid sequences, not nucleotide). This should be easy enough ...


2

So far, grabseqs is the easiest option, a wrapper for fastq_dump and fasterq-dump, you can install it with conda, I recommend you to use an environment: conda create -n grabseqs -c louiejtaylor -c bioconda -c conda-forge grabseqs conda activate grabseqs grabseqs sra SRRNNNNNNNN conda deactivate And download directly projects, runs, and bioprojects from ...


2

I see no option to specify the reference version using the NCBI dbSNP browser, it is set to download the latest built information. I think this is not the standard tool to download dbSNP data across many sites, but rather to browse it and visualize it for specific variation. If you are only interested in getting info for a smaller range of positions, I ...


1

From this SO post. You can use seqkit to remove duplicate sequences with the command below: seqkit rmdup -s < sequences.txt > out.fa The rmdup option removes duplicates, and the -s option calls duplicates on the basis of sequence, ignoring differences in headers.


1

NCBI Trace Archive The NCBI Trace Archive is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects. Contaning more than 2 billion traces.


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You can download the full db and and put out anything you want with your favourite scripting language. To do so, you need to request an account first. Once you log in, scroll down to the bottom of the download options. There are 2 meta-data download options, pick what you need.


1

Oh you silly sausage! Don't use AGP gap files. This is not a direct answer but a workaround. However, if your scaffolded genome is annotated, you might as well submit a flat file (.embl) instead of fasta and the gap file. The thing is, making that file is actually a lot more straightforward thanks to amazing EMBLmyGFF3. You will also need the locus tag (a ...


1

How about: http://www.informatics.jax.org/expression.shtml http://www.emouseatlas.org/emage/home.php Other potential databases of interest: https://biokeanos.com/search?q=co-expression+%2Bmouse


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If processing a huge table with lots of "false positives" is OK, then you could enter your search term, from top right choose "Send to" > "File" Format: "RunInfo".


1

ProTherm2 contains thermodynamic properties of proteins and mutants. https://www.iitm.ac.in/bioinfo/ProTherm2/ . NAR Database issue advertises it as containing melting temperatures. For the reference - found it with https://biokeanos.com/search?q=protein+%2Bmelting


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