FALDO-paper examples collation

[Jerven Bolleman]

Hi All,

I am going to to merge all the examples using the
circular Nicotiana tabacum chloroplast genome.

This seems to have most of the features that we use in examples.
And using a single ddbj record will make the examples somewhat smaller.

http://getentry.ddbj.nig.ac.jp/getentry/na/Z00044/?filetype=html

Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Peter Cock]

Hi Jerven,

A single example DDBJ/GenBank file sounds good - but it may not be
possible to find all the oddities in one file. I appreciate that a
prokayotic example wouldn't have introns/exons which would be a
drawback for a single unified example, so it does make sense to focus
on mitochondria and chloroplasts for this unifying example (circular
in order to address features spanning the origin).

Your suggested example does have an intron annotated as spanning the
origin. However, that Nicotiana tabacum chloroplast has no
trans-splicing - and a mixed strand tRNA gene is a wonderful complex
special case and in these examples (which unfortately lack an
origin-spanning gene).

I have found a few potential examples to use instead - what other
"special" features where you looking for?

Peter

-------------------------------------------------------------------------

After searching dozens of chloroplast examples here is a candidate:

http://www.ncbi.nlm.nih.gov/nuccore/NC_022383.1

LOCUS NC_022383 159954 bp DNA circular PLN 25-SEP-2013
DEFINITION Eucalyptus diversifolia chloroplast, complete genome.
...

gene complement(join(1..74,159954))
/locus_tag="EDIF_CP_t001"
/db_xref="GeneID:17080331"
tRNA complement(join(1..74,159954))
/product="tRNA-His"
/codon_recognized="CAC"
...

CDS join(74301..74414,complement(103154..103384),
complement(102581..102607))
/gene="rps12"
/locus_tag="EDIF_CP_p045"
/trans_splicing
/codon_start=1
/transl_table=11
/product="ribosomal protein S12"
/protein_id="YP_008575562.1"
/db_xref="GI:545716698"
/db_xref="GeneID:17080265"
/translation="MHPSTCSSTLRTSPKSGGFRDISDWLSCVSNKLFNSWHTITPKK
PNSALRKVARVRLTSGFEITAYIPGIGHNSQEHSVVLVRGGRVKDLPGVRYHIVRGTL
DAVGVKDRQQGRSQYGVKKPK"
...

Some of its sister species are similar, others lack the single base
origin overlap. Presumably this was a large batch orientated to have a
common origin which turned out during annotation to not be quite ideal
in these cases. (I was focussing on cases where multiple circles were
available from the same species or genus).

-------------------------------------------------------------------------

And here is a mitochondria candidate, Trichoplax adhaerens mitochondrion

http://www.ncbi.nlm.nih.gov/nuccore/NC_008151.2

LOCUS NC_008151 43079 bp DNA circular INV 23-APR-2010
DEFINITION Trichoplax adhaerens mitochondrion, complete genome.
...

gene join(42777..43079,1..3)
/gene="orf101"
/locus_tag="TradoM_p01"
/db_xref="GeneID:8174836"
CDS join(42777..43079,1..3)
/gene="orf101"
/locus_tag="TradoM_p01"
/codon_start=1
/transl_table=4
/product="hypothetical protein"
/protein_id="YP_003058391.1"
/db_xref="GI:254032037"
/db_xref="GeneID:8174836"
/translation="MLASHKKNDQRRLRRLDTFSVPNDQLGPQKMGSVGAHWFGGVPP
RRSLGGAEGSPRDPCRFKKRLPNKSTWRRLWRRGTPTRTRLTGPPQVGSCPPPQRKI"
...

CDS join(25202..25587,26044..26300,29255..29331,31942..31952,
41414..41506,complement(9991..10037),
complement(8734..8996),complement(7575..8045))
/gene="cox1"
/locus_tag="TradoM_p06"
/EC_number="1.9.3.1"
/exception="RNA editing"
/trans_splicing
/codon_start=1
/transl_table=4
/product="cytochrome c oxidase subunit I"
/protein_id="YP_654082.2"
/db_xref="GI:254032033"
/db_xref="GeneID:4126650"
/translation="MTSFVRWFFSCNHKDIGSLYLVFGALSGAIGTAFSMLIRLELSS
PGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMIGAPDMAFPRLNNIS
FWLLPPALFLLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSIL
GAMNFITTVMNMRTPGMTMSRIPLFVWSVFITAILLLLSLPVLAGAITMLLTDRNFNT
TFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISQILSLFSYKKQIFGYLGMVY
AMLAIGVLGFIVWAHHMFVVGMDVDTRAYFTAATMIIAVPTGIKIFSWLATVSGSGRN
LILTTPMAWALGFIFLFTIGGLTGIVLSNSSLDILLHDTYYVVAHFHFVLSMGAVFAI
FGGFYLWFGKITGYAYKDIYGLIHFWLMFIGVNITFFPQHFLGLAGLPRRYADYPDNF
EDFNQISSFGSVISLTAVIWFIVVIFDAYYREEPFDINTMAKGPLIPFSCQPAHFDTL
EWSLTSPPEHHTYNELPYIVGGPKSS"
...
etc

-------------------------------------------------------------------------

Here's a more extreme example, transplicing between different molecules:
http://www.ncbi.nlm.nih.gov/nuccore/JF750519.1 - Silene conica
chromosome 20 mitochondrion


Peter

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