AS DOWNLOADED FROM GRAMENE SITE:
http://www.gramene.org/documentation/Alignment_docs/cornsensus.html

The documentation here refers to file:
UnigeneToRice.txt, stored in this directory.

	
/* 

This documents the processing of zea mays Clusters and ESTs to the rice genome. 
Lenny Teytelman
Sun Dec  8 11:30:43 2002
*/

The BACs/PACs are from the GenBank Entrez Nucleotide query:

"Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC [ALL] OR 
chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA [TITL] OR mRNA [TITL]
 OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL] OR protein[TITL]))" for BACs, a
nd

The Dupont Unigene set is from http://www.agron.missouri.edu/files_dl/MMP/Cornse
nsus.fasta  The average Clusters and ESTs length is 1,000.



3,420 sequences were compared to  10,678 Clusters and ESTs using BLAT with minId
entity=50.   The 22,785 BLAT hits were filtered using pslReps utility with -sing
leHit parameter.  This resulted in 9,162 alignments.

The lengths of the matches are distributed as follows:

Length of
hits            Count
--------        ------
0-100           596
100-150         776
150-200         899
200-250         930
250-300         886
300-350         815
350-400         724
400-450         541
450-500         462
500-550         362
550-600         296
600-650         270
650-700         224
700-750         188
750-800         163
>800            1030



Removing matches with less than 150bp match-length leaves 7,770 hits.

Many of the Clusters and ESTs hit more than once.  The distribution of the hit f
requencies is:

# Of
Hits per
Feature         Count
-------         -----
01              5725
02              894
03              73
04              8
06              1



Clusters and ESTs that hit more than three times are removed, with 7,732 hits re
maining.  These matches have the following distribution of the percent identity 
per hit:

% Identity      Count
----------      ----------
43              1
53              2
55              1
58              1
60              1
61              1
62              2
63              1
64              2
65              2
66              7
67              5
68              3
69              7
70              18
71              18
72              13
73              21
74              35
75              33
76              63
77              64
78              104
79              119
80              176
81              195
82              296
83              354
84              457
85              586
86              731
87              820
88              896
89              870
90              708
91              485
92              303
93              168
94              69
95              54
96              19
97              13
98              8


The distribution of the sequenced clone gaps is:

Bac Gap
Length          Count
------          ----------
01000           5000
02000           1458
03000           715
04000           262
05000           117
06000           39
07000           30
08000           23
09000           15
10000           12
20000           31
30000           9
40000           8
50000           4
60000           7
70000           1
>90000          1


The hits represent 6,692 unique Clusters and ESTs (62% of the total 10,678) and 
2,503 sequenced clones  (73% of the 3,420).  Those having at least one gap of le
ngth 50 or above, are considered multi-exon hits.  5,888 are multi-exon and 817 
are single-exon hits. 



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Last modified: Thu Jan 23 17:03:12 2003