Genome Annotation - Finding Genes Program

Question

[Daniel Fernández]

Hi,

May be my question is very simple, I want to find some genes in a eukaryotic genome, I have my genes (mRNA - sheep, cattle, goat, human) and a genome (alpaca) in multifasta, I tried with homology-based programs, AAT and GeneSeqer, but they don't give me a GFF output, ATT gave me a alignment and a statistics files for each genomic sequence, so It gave me to many files, and GeneSeqer gave me a statistics and alignment in one file, I would to have only one statistics file, with the start end position, and a GFF output. Any ideas?

Answer 1

[Yannick Wurm]

Use MAKER.

[Daniel Fernández]

Well I was trying to install the MAKER this days, the program is very complete it use many prograsm and the Exonarate too, but for me is a little difficult to install it, this need some prerequisites, DBI, DBD::SQLite, Proc::ProcessTable, threads, IO::All and IO::Prompt; I installed all except DBD::SQLite and IO::All, in its README file did not say how to, maybe is like the others, (perl Makefile.PL; make; make test; make install) but I don't sure, I don't want to spoil the installation, can you tell how I can installed that, please?.

[Yannick Wurm]

Indeed, one issue with using PERL (Maker is in PERL) are the weird dependencies. I don't remember what exactly I did or needed. If you have specific problems the best place is the maker mailing list: https://groups.google.com/forum/?fromgroups#!forum/maker-devel

Answer 2

[Leszek]

Exonerate will do the job. It can align genes, mRNA, proteins, EST, or genome to genome.

It outputs GFF (--showtargetgff yes).

The set of parameters I use (fungal genomes):

--showvulgar yes
--softmaskquery yes
--softmasktarget yes
--minintron 20
--maxintron 3000
--ryo ">%qi length=%ql alnlen=%qaln>%ti length=%tl alnlen=%taln"
--showalignment no
--showtargetgff yes
--bestn 5
--percent 70