Mitochondrial annotation tools other than MITOS and DOGMA

Question

[juhi.capricon]

Hi All

I am working on de novo mitochondrial genome assembly of trematode species. The size of the assembled genome is ~14kb which is also expected, considering the genome size of the closest reference.

I used MITOS for gene prediction, but some of the genes are reported as split/duplicated in the result. And when the predicted split proteins (from MITOS) were aligned against the NR database using BLASTP they got aligned to the protein other than the predicted one. So I am not sure of the result and want to cross check annotation with other tools as well.

I have already tried with MITOS and DOGMA, so please let me know the names of other trematode mitochondrial genome annotation tools for gene prediction.

Thank you

[GenoMax]

Use Mauve to see what your genome looks like against the closest relative at hand. That should give you some indication of the quality of your assembly.

[mks002]

Hello all,

I was also working on the insect mitochondrial genome. The sample is an amber preserved sample. I wanted to predict all the 37 genes. Some trna were missing in prediction from MITOS and DOGMA.

My question , why i am seeing gap in my gene prediction (2000 bp) i.e in the whole genome of ~15kb there 13kb which composing the rrna, trna and protein coding. Around ~500 bp would the control or D-loop region. Still 1500 bp is not covered ?

The assembly looks fine and it matched ~80% to the thrips mitochondrial genome. I would be thankful for the suggestion.

[mks002]

Juhi u can check with getorf or the Orf finder with correct genetic code.

Answer 1

[Juke34]

I started a list of tools to annotate mitochondria here: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_mitome.md

Usually I use 2 / 3 different tools, I map external evidence (e.g proteins from mitochondrion database) and I load everything into a genome browser like Webapollo, and I do manual curation.

Answer 2

[bernt.matthias]

The best suggestion in cases of problems with (scientific) software is to contact the authors (the above suggestions are also very good).

Also you might want to give MITOS2 a try which was recently put online.

Answer 3

[ashotmarg2004]

MitoZ is another option, it worked quite well for some of my vertebrate as well as insect species! https://github.com/linzhi2013/MitoZ

[sunnykevin97]

Thanks for the post, MitoZ works well for vertebrate genomes. Able to find the contigs belonging to the mitogenome.