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General Description:
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ParaRNA is a software for computing parametric alignment of
two RNA structures. It takes two RNA secondary
structures and match score, indel
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score, the range of mismatch score
and the range of gap score as its input, and computes all the optimal
alignments in the parametric space given by
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mismatch score and gap score, and show them in a graphic
interface.
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Nucleotide
(also called base) is one of {A,U,G,C}, and a base pair
is two paired nucleotides.
A RNA structure is constituted by R and P, where R |
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sequence of nucleotides and P is a set of base pairs. So
we can express a RNA secondary structure like this: R=AAGUCUAGGUCUCACU, |
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P={(1,5),(2,4),(7,12),(8,10),(13,15)}.(We use the position of the
nucleotide in R to delegate the nucleotide and its position is numbered
from 0.) |
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convenience, we use three integers to express a stem (which is nested
pairs and among these pairs there is no other base): the first integer
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the left-end base of the stem, the second integer represents the
right-end base of the stem and the last integer expresses the number of
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in the stem. So we can
express the above RNA secondary structure like this: R=AAGUCUAGGUCUCACU,P=1
5 2 7 12 1 8 10 1 13 15 1. |
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In
our software, we input
the RNA secondary structure like the following examples:
5Srna-b_B.sub_matured_RCS
GCTTGGCGGC GTCCTACTCT
CACAGGGGGA
AACCCCCGAC
TACCATCGGC GCTGAAGAGC
TTAACTTCCG
TGTTCGGTAT
GGGAACGGGT GTGACCTCTT
CGCTATCGCC ACCAAA
>
>
(1 )
1
115 10
(2 ) 12
48 11
(3 ) 24
36
5
(4 ) 50
102 2
(5 ) 53
100 6
(6 ) 63
89 2
(7 ) 67
87
4
>
5Srna+b_B.sub_matured
TTTGGTGGCG AUAGCGAAGA GGTCACACCC
GTTCCCATAC
CGAACACGGA AGTTAAGCTC
TTCAGCGCCG
ATGGTAGTCG GGGGTTTCCC
CCTGTGAGAG TAGGACGCCG
CCAAGC
>
>
(1 )
0
114 10
(2 ) 13
65
2
(3 ) 15
62
6
(4 ) 26
52
2
(5 ) 28
48
4
(6 ) 67
103 11
(7 )
79
91
5
>
and give the output as follows:
The first RNA secondary
structure is:
GCTTGGCGGCGTCCTACTCTCACAGGGGGAAACCCCCGACTACCATCGGCGCTGAAGAGCTTAACTTCCGTGTTCGGTATGGGAACGGGTGTGACCTCTTCGCTATCGCCACCAAA
1 115 10 12 48 11 24 36 5 50 102 2 53 100 6 63 89 2 67
87 4
The second RNA secondary structure is:
TTTGGTGGCGAUAGCGAAGAGGTCACACCCGTTCCCATACCGAACACGGAAGTTAAGCTCTTCAGCGCCGATGGTAGTCGGGGGTTTCCCCCTGTGAGAGTAGGACGCCGCCAAGC
0 114 10 13 65 2 15 62 6 26 52 2 28 48 4 67 103 11 79 91
5
Match score is:1
Indel score is:0.500
Mismatch score range is [ 0 , 2 ]
Gap score range is [ 0 , 2 ]
There are 5 optimal alignments in parametric space:
The 1 optimal alignment is:
Match Number:14
Mismatch Number:6
Indel Number:32
Gap Number:18
Pair Match Number:22
Pair Mismatch Number:2
Pair Indel Number:32
G|C|T|T|G|G|C|G|G|C|G|T|C|C|T|A|C|T|C|T|C|A|C|A|G|G|G|G|G|A|A|A|C|C|C|C|C|G|A|C|T|A|C|C|A|T|C|G|G|C|G|C|T|G|A|A|G|A|G|C|T|T|A|_|A|C|T|T|C|C|G|T|G|T|T|C|_|_|_|G|G|T|A|_|_|T|G|G|G|A|_|_|A|C|G|G|_|_|G|T|G|T|G|A|C|C|T|C|T|T|C|_|G|C|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|T|A|T|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|C|G|C|C|A|C|C|A|A|A|_|
_|T|T|T|G|G|T|G|G|C|G|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|U|A|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|G|C|_|G|A|A|G|A|G|G|T|C|A|C|A|C|_|_|C|C|G|T|_|_|T|C|C|C|A|_|_|T|A|C|C|_|_|_|G|A|A|C|A|C|G|G|A|A|G|T|_|T|A|A|G|C|T|C|T|T|C|A|G|C|G|C|C|G|A|T|G|G|T|A|G|T|C|G|G|G|G|G|T|T|T|C|C|C|C|C|T|G|T|G|A|G|A|G|T|A|G|G|A|C|G|C|C|G|C|C|A|A|G|C|
The 2 optimal alignment is:
Match Number:10
Mismatch Number:17
Indel Number:18
Gap Number:12
Pair Match Number:22
Pair Mismatch Number:2
Pair Indel Number:32
G|C|T|T|G|G|C|G|G|C|G|T|C|C|T|A|C|T|C|T|C|A|C|A|G|G|G|G|G|A|A|A|C|C|C|C|C|G|A|C|T|A|C|C|A|T|C|G|G|C|G|C|T|G|A|A|G|A|G|C|T|T|A|_|A|C|T|T|C|C|G|T|G|T|T|C|G|G|T|A|T|G|G|G|A|A|C|G|G|_|_|G|T|G|T|G|A|C|C|T|C|T|T|C|_|G|C|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|T|A|T|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|C|G|C|C|A|C|C|A|A|A|_|
_|T|T|T|G|G|T|G|G|C|G|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|U|A|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|G|C|_|G|A|A|G|A|G|G|T|C|A|C|A|C|_|_|C|C|G|T|T|C|C|C|A|T|A|C|C|G|A|A|C|A|C|G|G|A|A|G|T|_|T|A|A|G|C|T|C|T|T|C|A|G|C|G|C|C|G|A|T|G|G|T|A|G|T|C|G|G|G|G|G|T|T|T|C|C|C|C|C|T|G|T|G|A|G|A|G|T|A|G|G|A|C|G|C|C|G|C|C|A|A|G|C|
The 3 optimal alignment is:
Match Number:14
Mismatch Number:12
Indel Number:20
Gap Number:14
Pair Match Number:22
Pair Mismatch Number:2
Pair Indel Number:32
G|C|T|T|G|G|C|G|G|C|G|T|C|C|T|A|C|T|C|T|C|A|C|A|G|G|G|G|G|A|A|A|C|C|C|C|C|G|A|C|T|A|C|C|A|T|C|G|G|C|G|C|T|G|A|A|G|A|G|C|T|T|A|_|A|C|T|T|C|C|G|T|G|T|T|C|G|G|T|A|T|G|G|G|A|_|A|C|G|G|_|_|G|T|G|T|G|A|C|C|T|C|T|T|C|_|G|C|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|T|A|T|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|C|G|C|C|A|C|C|A|A|A|_|
_|T|T|T|G|G|T|G|G|C|G|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|U|A|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|G|C|_|G|A|A|G|A|G|G|T|C|A|C|A|C|_|_|C|C|G|T|_|T|C|C|C|A|T|A|C|C|G|A|A|C|A|C|G|G|A|A|G|T|_|T|A|A|G|C|T|C|T|T|C|A|G|C|G|C|C|G|A|T|G|G|T|A|G|T|C|G|G|G|G|G|T|T|T|C|C|C|C|C|T|G|T|G|A|G|A|G|T|A|G|G|A|C|G|C|C|G|C|C|A|A|G|C|
The 4 optimal alignment is:
Match Number:14
Mismatch Number:0
Indel Number:44
Gap Number:26
Pair Match Number:22
Pair Mismatch Number:1
Pair Indel Number:34
G|C|_|T|T|G|G|C|G|G|C|G|T|C|C|T|A|C|T|C|T|C|A|C|A|G|G|G|G|G|A|A|_|A|C|C|C|C|C|G|A|C|T|A|C|C|A|T|C|G|G|C|G|C|T|G|A|A|G|A|G|_|_|C|T|T|A|_|A|C|T|T|C|C|G|T|G|T|T|C|_|_|_|G|G|T|A|_|_|T|G|G|G|A|_|_|A|C|G|G|_|_|G|T|G|T|_|_|G|A|C|C|T|C|T|T|C|_|G|C|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|T|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|T|C|G|C|C|A|C|C|A|A|A|_|_|
_|_|T|T|T|G|G|T|G|G|C|G|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|U|A|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|G|C|_|G|A|A|G|A|G|G|T|C|_|_|A|C|A|C|_|_|C|C|G|T|_|_|T|C|C|C|A|_|_|T|A|C|C|_|_|_|G|A|A|C|A|C|G|G|A|A|G|T|_|T|A|A|G|_|_|C|T|C|T|T|C|A|G|C|G|C|C|G|A|T|G|G|T|A|G|T|C|G|G|G|G|G|T|T|T|C|C|C|C|C|T|G|T|G|A|G|A|G|T|A|G|G|A|_|C|G|C|C|G|C|C|A|A|_|G|C|
The 5 optimal alignment is:
Match Number:14
Mismatch Number:0
Indel Number:44
Gap Number:30
Pair Match Number:22
Pair Mismatch Number:0
Pair Indel Number:36
G|C|_|T|T|G|G|C|_|G|G|C|G|T|C|C|T|A|C|T|C|T|C|A|C|A|G|G|G|G|G|A|_|A|A|C|C|C|C|C|G|A|C|T|A|C|C|A|T|C|G|G|C|G|C|T|G|A|A|G|A|G|_|_|C|T|T|A|_|A|C|T|T|C|C|G|T|G|T|_|_|_|_|T|_|_|C|G|G|T|A|T|G|G|G|A|_|A|C|G|G|_|_|G|T|G|T|_|_|G|A|C|C|T|C|T|T|C|_|G|C|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|T|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|T|C|G|C|C|_|A|C|C|A|A|A|_|_|
_|_|T|T|T|G|G|_|T|G|G|C|G|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|A|U|A|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|G|C|_|G|A|A|G|A|G|G|T|C|_|_|A|C|A|C|_|_|C|C|G|T|_|T|C|C|C|A|T|A|C|C|G|_|_|A|_|_|_|_|A|C|A|C|G|G|A|A|G|T|_|T|A|A|G|_|_|C|T|C|T|T|C|A|G|C|G|C|C|G|A|T|G|G|T|A|G|T|C|G|G|G|G|G|T|T|T|C|C|C|C|C|T|G|T|G|A|G|A|G|T|A|G|G|A|_|C|G|C|C|G|_|C|C|A|A|_|G|C|
It is free for non-commercial use subject to copyright
restrictions.
Download the
Executive file:
Please click
here to download the software (for windows XP, windows 2000). ¡¡ |