How do I rebuild the files 12S.mito.aln and 16S.mito.aln?

[sjackman]

I'm interested in building a plant mitochondrial database. Its rRNA are 5S, 18S and 26S
See #2

[tseemann]

Good question @sjackman

What is the top-most level of the NCBI taxonomy that encompasses the "plant" family you are interested?

There are no plant sequences here: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/

Looking at A.thalania mtDNA I see it has thse genes you say, with some semi-standardised alternate names?

                     /gene="rrn26"
                     /product="26S ribosomal RNA protein"

                     /gene="rrn18"
                     /product="18S ribosomal RNA"

                     /gene="rrn5"
                     /product="5S ribosomal RNA"

I think the 5S and 18S are similar to other ones. But the 26S seems very diverse?

[sjackman]

Viridiplantae? I've been using this search to get a list of species.

esearch -db nuccore -query 'Viridiplantae[Organism] mitochondrion[Title] (complete genome[Title] OR complete sequence[Title])'

https://www.ncbi.nlm.nih.gov/nuccore/?term=Viridiplantae%5BOrganism%5D%20mitochondrion%5BTitle%5D%20(complete%20genome%5BTitle%5D%20OR%20complete%20sequence%5BTitle%5D)

[sjackman]

RFAM has alignments of rrn5, rrnS, and rrnL
Here are the RFAM bacterial family and clans for rrnS and rrnL. The clans include the families for other kingdoms. The bacterial families identify plant mitochondrion rrnS and rrnL.

5S_rRNA (RF00001) http://rfam.xfam.org/family/RF00001
5S_rRNA (CL00113) http://rfam.xfam.org/clan/CL00113

SSU_rRNA_bacteria (RF00177) http://rfam.org/family/RF00177
SSU (CL00111) http://rfam.org/clan/CL00111

LSU_rRNA_bacteria (RF02541) http://rfam.org/family/RF02541
LSU (CL00112) http://rfam.org/clan/CL00112

See #2 (comment)