|
|
|
Gene matches to maize genomic sequences
Matches to translated sequences
The AZM (Assembled Zea mays) and singleton sequences from maize methylation
filtered and high Cot genomic DNA clones were compared to several protein and DNA
transcript databases, using BLAT [3].
We searched the TIGR non-redundant amino acid database (nraa), plant Gene Indices,
and plant High Throughput cDNAs (HTCs) in GenBank to determine the number of
significant hits.
Using the comparison process illustrated
here,
we were able to calculate the number of AZMs and singletons that had a significant
match to a protein or other transcript.
| |
Number of AZM/singleton
sequences |
% AZM/singleton matching a protein |
% AZM/singleton matching a TC/EST |
| Release 4.0MF | 133,806 | 24% | 24% |
|---|
| Release 4.0HC | 172,600 | 28% | 22% |
|---|
| Release 4.0ALL | 243,807 | 21% | 18% |
|---|
| Release 4.0UF | 49,643 | 1.0% | 4.4% |
|---|
Matches to maize characterized proteins
A set of characterized maize proteins was produced from the TIGR non-redundant
amino acid database (nraa) by filtering out uncharacterized maize proteins
e.g. those proteins described as 'unknown', 'unnamed', 'unassigned',
'hypothetical', etc. We then calculated the number of AZMs and singletons
having a significant match to a characterized maize proteins.
| |
% Characterized maize proteins matching AZM/singletons
(Characterized maize proteins = 2,283) |
Summary
diagram |
| Release 4.0MF | 42% |
view |
|---|
| Release 4.0HC | 39% |
view |
|---|
| Release 4.0ALL | 48% |
view |
|---|
| Release 4.0UF | 2.2% |
view |
|---|
|
