Hi,
I am new with Diamond. Diamond seems to be good as a sequence aligner for protein and translated DNA searches.
I only a concern. Where can I download .fasta files to build up a database?
Is the following database the best one? ftp://ftp.ncbi.nlm.nih.gov/blast//db/FASTA/nr.gz
Do you know the link of others curated databases?
Thanks a lot
Luigi
Hi Luigimaria,
I would recommend you first to check what sequences and categories includes the databases before just downloading any of them.
I will put here the links for three sequences databases that I normally use, but please read about them before doing serious work with them:
Pfam: http://pfam.xfam.org/
db link: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.fasta.gz
Swiss prot: https://web.expasy.org/docs/swiss-prot_guideline.html
db link: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
UniProt90: https://www.uniprot.org/help/uniref
db link: ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
In every case you will have a fasta file with sequences, that I hope you will be able to use to construct a DIAMOND database. If not just let me know.
Best regards.
NR is the NCBI protein database, which is not manually curated and is redundant. Use Swiss prot or any other manually curated database or if your protein is from model organism, use its own Ensemble database. You can use any of the above mentioned databases but, keep in mind the advice from Salvador Ramirez-Flandes
Nevertheless, SURE, you can use NR database from NCBI, there are many use it, and I use it too. But one must know the purpose and right way to use any database. Wrong use of even good database and parameters can cause confusion in analysis.
Thanks a lot for the usefull answers.
I have one question more, what about keeg database? Where can I download the entire database? I have used it via mg-rast and it seems fix very well for my aims...
Thanks a lot for the usefull answers.
I have one question more, what about keeg database? Where can I download the entire database?
One year ago, I used it via mg-rast and it was perfect for my work...
Hi luigimaria,
Unfortunately, the KEGG database is not free for that purpose. MG-RAST has a license and thus it can be used through its website. You buy however the license in the KEGG website if you need it. It cost about US $5000 the license for an organization and US $ 1000 the personal alternative. I hope that helps. Best regards.
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