SEQXTANT README

seqxtant organizes related genomic sequences in order to study orthologs and paralogs in greater detail.

Overview

• Install ab-blast via https://www.advbiocomp.com personal license
• Get grimoire from KorfLab GitHub
• Get seqxtant from KorfLab GitHub
• Create a directory where you want to store the seqxtant database files
• Point SEQXTANT to the database directory or use the --env option
• Download genomic fasta, masked, and gff3 files for your favorite genomes
• Use seqxtant create to make a new database
• Use seqxtant add to add fasta and gff files to database
• Use seqxtant status to get information about the database
• Use seqstant validate to check overall genome stats
• Use seqxtant cluster to cluster related sequences...

Database

The "database" is a file called seqxtant.json that lives inside a directory that is either specified by an environment variable or passed in with the --env option. Probably should be a sqlite database...

Fasta and GFF3

GFF isn't actually used yet. The only thing that will be required someday will be the genes, so very large files should be filtered.

Dev Notes

All files downloaded from Ensembl for consistency.

Some clades used for testing:

• worms via Ensembl Metazoa
  • C. brenneri 3305
  • C. briggsae 367
  • C. elegans 7
  • C. japonica 18817
  • C. remanei 3670
• plants via Ensembl Plants
  • A.thaliana 7
  • O.sativa 63
  • P.patnes 357
  • P.vulgaris 708
  • P.trichocarpa 46
  • S.lycopersicum 2148
  • V.vinifera 22
• flies via Ensembl Metazoa
  • D.ananassae 13749
  • D.erecta 5124
  • D.grimshawi 17740
  • D.melanogaster 1870
  • D.mojavensis 6841
  • D.pseudoobscura 4790
  • D.sechellia 14730
  • D.simulans 7619
  • D.virilis 13530
  • D.willistoni 14838
  • D.yakuba 8122