README

Last updated on September 21, 2007

There are 22 tab-delimited files in this folder, each with a multiple alignment
of mitochondrially encoded tRNAs from tetrapod species. The tab-delimited fields
in the file represent the species scientific name, the common name, the
phylogenetic classification and the tRNA sequence and annotation, respectively.
The flanking regions of the tRNA genes are not aligned. In the annotation, the
"|" symbols delineate secondary structure elements in the mt-tRNAs according to
the prediction of the multiple alignment following Helm et al (2001). The
secondary structure prediction made by mfold is annotated with capital and
lowercase letters, with the capital letters representing paired nucleotides,
which roughly recapitulate the annotation made with the alignment. Each file
contains 277 lines with the species in the same order in each file.

A	Ala
C	Cys
D	Asp
E	Glu
F	Phe
G	Gly
H	His
I	Ile
K	Lys
L1	LeuUUR
L2	LeuCUN
M	Met
N	Asn
P	Pro
Q	Gln
R	Arg
S1	SerUCN
S2	SerAGY
T	Thr
V	Val
W	Trp
Y	Tyr

1. Helm M, Brule H, Friede D, Giege R, Putz D, Florentz C: Search for
characteristic structural features of mammalian mitochondrial tRNAs.
RNA 2000, 6:1356-1379.