[maker-devel] getting protein sequences from genomes

[Luciano Abriata]

Hello, I am trying to use Maker to annotate genomes from different individuals of a population (D. melanogaster flies).

My ultimate goal is to get, for each gene, the amino acid sequences of the coded proteins as they are expressed from each genome. My questions are:

1) How can I match proteins predicted for the same gene in two genomes?

2) What is the meaning of all the data in a line such as the following one (taken from the protein.fasta output)

maker-2L-augustus-gene-0.19-mRNA-1 protein AED:0.0322873164323667 eAED:0.0322873164323667 QI:2|1|0.66|1|1|1|3|208|541

3) If I include snap and augustus to improve protein predictions, I get several protein.fasta files: augustus_masked.proteins.fasta , snap_masked.proteins.fasta , non_overlapping_ab_initio.proteins.fasta , and proteins.fasta

Which of these files contains the definite set of predicted protein sequences?


Thanks in advance!

Luciano
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