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Difference between revisions of "mutateNA.pl"
From MMTSB
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== Description == | == Description == | ||
| + | Allows the mutation of nucleotides in nucleic acids. Mutation of double-stranded DNA maintains better intra-strand hydrogen bonding if base pairs are mutated | ||
| + | together (see example below) rather than mutating each strand separately. | ||
| + | <BR> | ||
| + | |||
| + | For RNA, the option <B>-rna</B> should be used. | ||
== Options == | == Options == | ||
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== Examples == | == Examples == | ||
| + | |||
| + | <mmtsbToolExample cmd="mutateNA.pl" set="test1"></mmtsbToolExample> | ||
| + | |||
| + | <mmtsbToolExample cmd="mutateNA.pl" set="test2"></mmtsbToolExample> | ||
Latest revision as of 15:42, 29 July 2009
Usage
usage: mutateNA.pl [options] [PDBfile]
options: [-seq [chain]index:[complementary:]sequence[=index:sequence]]
[-rna]
Description
Allows the mutation of nucleotides in nucleic acids. Mutation of double-stranded DNA maintains better intra-strand hydrogen bonding if base pairs are mutated
together (see example below) rather than mutating each strand separately.
For RNA, the option -rna should be used.
Options
- -help
- usage information
- -seq [chain]index:[complementary:]sequence[=...]
- nucleotide sequence to be mutated to
- -rna
- generate RNA instead of DNA
Examples
mutateNA.pl -seq A1:AT 1bna.chainA.pdb
mutate the first two nucleotides to AT in single-stranded DNA
ATOM 5 O5' ADE A 1 18.935 34.195 25.617 1.00 64.35 ATOM 6 C5' ADE A 1 19.130 33.921 24.219 1.00 44.69 ATOM 7 C4' ADE A 1 19.961 32.668 24.100 1.00 31.28 ATOM 8 O4' ADE A 1 19.360 31.583 24.852 1.00 37.45 ATOM 9 C3' ADE A 1 20.172 32.122 22.694 1.00 46.72 ATOM 10 O3' ADE A 1 21.350 31.325 22.681 1.00 48.89 ATOM 11 C2' ADE A 1 18.948 31.223 22.647 1.00 30.88 ATOM 12 C1' ADE A 1 19.231 30.482 23.944 1.00 36.58 ATOM 13 N9 ADE A 1 18.054 30.234 24.144 1.00 40.51 ATOM 13 C5 ADE A 1 16.102 29.236 24.585 1.00 40.51 ...
mutateNA.pl -seq A5:B8:TTAA 1bna.dna.pdb
mutates the central four base pairs (chain A: residues 5 to 8, chain B residues 8 to 5) to (TTAA):(AATT)
ATOM 5 O5' CYT A 1 18.935 34.195 25.617 1.00 64.35 ATOM 6 C5' CYT A 1 19.130 33.921 24.219 1.00 44.69 ATOM 7 C4' CYT A 1 19.961 32.668 24.100 1.00 31.28 ATOM 8 O4' CYT A 1 19.360 31.583 24.852 1.00 37.45 ATOM 9 C3' CYT A 1 20.172 32.122 22.694 1.00 46.72 ATOM 10 O3' CYT A 1 21.350 31.325 22.681 1.00 48.89 ATOM 11 C2' CYT A 1 18.948 31.223 22.647 1.00 30.88 ATOM 12 C1' CYT A 1 19.231 30.482 23.944 1.00 36.58 ATOM 13 N1 CYT A 1 18.070 29.661 24.380 1.00 40.51 ATOM 14 C2 CYT A 1 18.224 28.454 25.015 1.00 16.62 ...