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Next: Parallel execution Up: DeepForest: a Molecular Evolutionary Previous: Tree of amino acid

Automatic tree annotation from a given sequence database

In reconstruction of phylogenetic trees, automatic annotation from a given sequence database is quite important. One of our objects is inference of evolution by means of interpreting a phylogenetic tree rather than reconstruction of a phylogenetic tree itself. In this sense, annotation of the tree is an essential process in this study. However, when the number of sequences is large, it is virtually impossible to annotate without erroneous description by hand. The automatic annotation will make us free from such difficulty.

In DeepForest, annotating trees is carried out as follows:

1.
From a given database, a structured database is generated. This database has a hierarchy for records.

2.
ENTRY and TITLE fields are extracted.

3.
A description table is generated from ENTRY and TITLE fields.

4.
A tree is annotated according to this table.

Programs make_destbl and make_ph have been prepared to annotate a tree. When we have a tree in the phylip format, for example mhc.phb, this tree is annotated as follows:



make_records mhc.dat mhc.pl
extract_fields mhc.pl mhc.ent.pl ENTRY TITLE
make_destbl mhc.ent.pl mhc.des
# In the current version, some operations are needed by hand here.
# Replace all parentheses with square brackets, and replace all
# commas with slashes in mhc.des.
make_ph mhc.des mhc.phb mhc.des.phb



An annotated tree (mhc.des.phb) is shown in fig. 1.3.


next up previous
Next: Parallel execution Up: DeepForest: a Molecular Evolutionary Previous: Tree of amino acid
Satoshi OOta
1999-03-06