Dear all, I’m learning this tutorial:NCBI BLAST+ against the MAdLand
but I can find the MadLandDB in my local server, how can i get them?
pls kindly help on this. Thanks a lot.
Hello @linsen_hou
The source of the data is listed at the top of the tutorial. You’ll need to either install that database on your server or add it as a fasta to your history to use as a custom genome.
You could also try contacting the tutorial author directly through GitHub.
Introduction
MAdLandDB is a protein database comprising of a comprehensive collection of fully sequenced plant and algal genomes, with a particular emphasis on non-seed plants and streptophyte algae. Additionally, for comparative analysis, the database also includes genomes from various other organisms such as fungi, animals, the SAR group, bacteria, and archaea. The database is actively developed and maintained by the Rensing lab and released in the MAdLand setting. It employs a system of species abbreviation using a 5 letter code, which is constructed using the first three letters of the genus and the first two letters of the species name, for example, CHABR for Chara braunii. Furthermore, the database provides gene identification through the addition of gene ID’s and supplementary information such as the encoding source of the gene, whether it is plastome encoded (pt) or transcriptome-based (tr) in cases when a genome is not yet available. The key advantage of this database is its non-redundant nature, and the fact that all sequences are predominantly from genome projects, thereby increasing their reliability.
Got it , thanks for your kindly reply, I’ll try it.