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Updated readme content. Ready to release
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fortune9 committed May 4, 2015
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30 changes: 19 additions & 11 deletions README
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Expand Up @@ -13,20 +13,26 @@ more often than other synonymous ones in highly expressed genes
(I<Sharp and Li 1987>). To measure the unevenness of codon usage, multiple
indices of codon usage bias have been developed, such as Fop
(Frequency of optimal codons), CAI (Codon Adaptation Index), tAI (tRNA
Adaptation Index), and ENC (Effective Number of Codons). The causes of
CUB phenomena are complicated, including, mutational bias, selection
on translational efficiency or accurancy. CUB is one fundamental concept
in genetics.
Adaptation Index), and ENC (Effective Number of Codons). Biased codon
usage is widespread, visible in all species. It is important both to
identify codons having high translational efficiency (often named
optimal codons) and to study the distribution of codon usage among
genes (e.g., genes with more optimal codons versus genes with fewer
optimal codons).

So far, no software exists to compute all the above CUB indices, and
worse is that parameters of CUB calculations are often fixed in
software, so one can only analyze genes in a limited list of species
and one can not incorporate its own parameters such as sequences of
highly expressed genes in a tissue.
it is worse that parameters in existing software are often fixed,
so one can compute certain types of CUB indices for a limited list of
species and can not modify parameters. For example, when one wants to
identify optimal codons in certain tissues, it may be better to use
most highly expressed genes to calculate CAI index, which is
impossible with existing software.

This package mainly solves these two problems. We also extend some
methods, such as GC-content corrected ENC, background-data normalized
CAI, etc. See the relevant methods in CUB classes for more details.
This package mainly solves these two problems: providing tools
computing all common CUB indices and allowing users to tune parameters
freely. We also incorporate or extend some method variants, such as
GC-content corrected ENC, background-data normalized CAI, etc.
See the relevant methods' description in CUB classes for more details.


3. INSTALLATION
Expand Down Expand Up @@ -63,6 +69,8 @@ You can also look for information at:
http://search.cpan.org/dist/Bio-CUA/


You can also email me at zhangz.sci@gmail.com for help.

5. LICENSE AND COPYRIGHT

Copyright (C) 2015 Zhenguo Zhang
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94 changes: 47 additions & 47 deletions t/cai.out
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@@ -1,59 +1,59 @@
CCA 0.587301587301587
CTG 1
AAT 0.604477611940298
CCT 0.407407407407407
GAT 0.892857142857143
TAC 1
ACA 0.469767441860465
TTA 0.0857908847184987
CGA 0.364864864864865
GAG 1
ATC 1
CTC 0.386058981233244
TAT 0.537634408602151
ATA 0.284518828451883
CCC 1
CTT 0.142091152815013
CAG 1
TTC 1
GTC 0.565610859728507
TCT 0.191881918819188
ACG 0.744186046511628
ACC 1
TGT 0.23
CTA 0.190348525469169
CAA 0.380352644836272
GCG 0.47787610619469
TAT 0.537634408602151
TTT 0.450261780104712
TGC 1
GTT 0.330316742081448
TAC 1
GTG 1
ATT 0.414225941422594
AGA 0.243243243243243
CTA 0.190348525469169
AAT 0.604477611940298
TGT 0.23
TTA 0.0857908847184987
AGC 1
GCA 0.274336283185841
CTG 1
GGT 0.335616438356164
CTT 0.142091152815013
GTA 0.194570135746606
GGG 0.174657534246575
AGT 0.450184501845018
ACT 0.288372093023256
GAT 0.892857142857143
CAC 1
TTC 1
AAA 0.398576512455516
CCT 0.407407407407407
TTG 0.329758713136729
CGC 1
GAG 1
AGG 0.310810810810811
CGG 0.540540540540541
TCA 0.254612546125461
GCT 0.309734513274336
AAC 1
GTT 0.330316742081448
AAG 1
AGA 0.243243243243243
TCC 0.845018450184502
ACG 0.744186046511628
CCG 0.878306878306878
GGA 0.537671232876712
GAA 0.394927536231884
CGT 0.371621621621622
CGC 1
CGG 0.540540540540541
GGC 1
CAA 0.380352644836272
AGC 1
CAT 0.537688442211055
GGA 0.537671232876712
GAC 1
CCG 0.878306878306878
GTG 1
GCC 1
AAG 1
CGT 0.371621621621622
ACA 0.469767441860465
ACC 1
TTG 0.329758713136729
GAA 0.394927536231884
TCG 0.712177121771218
GAC 1
CAG 1
GGG 0.174657534246575
GCG 0.47787610619469
GCT 0.309734513274336
GTA 0.194570135746606
TTT 0.450261780104712
GTC 0.565610859728507
ATC 1
ATA 0.284518828451883
TCA 0.254612546125461
CCA 0.587301587301587
CAT 0.537688442211055
TCT 0.191881918819188
AAC 1
GCA 0.274336283185841
CAC 1
AAA 0.398576512455516
ACT 0.288372093023256
98 changes: 49 additions & 49 deletions t/tai.out
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@@ -1,60 +1,60 @@
CTA 0.0956261950286807
GTG 0.365200764818356
ATT 0.430210325047801
TAC 0.430210325047801
AGA 0.1434034416826
CCC 0.240917782026769
TGC 0.334608030592734
GTT 0.286806883365201
CGA 0.478059273422562
ATC 0.309751434034417
CTC 0.17208413001912
TAT 0.253824091778203
GCA 0.09565965583174
CTG 0.413001912045889
TTA 0.191204588910134
AGC 0.286806883365201
AAT 0.338432122370937
TGT 0.197418738049713
ATA 0.0956453154875717
CCC 0.240917782026769
CTT 0.239005736137667
ACG 0.235181644359465
GTC 0.206500956022945
CAG 0.443594646271511
TCT 0.382409177820268
TTC 0.382409177820268
AAA 0.286806883365201
ACC 0.309751434034417
TGT 0.197418738049713
CCA 0.239039196940727
AAT 0.338432122370937
CTG 0.413001912045889
CCT 0.334608030592734
GAT 0.394837476099426
CAC 0.239005736137667
ACA 0.286849904397706
TTA 0.191204588910134
TAC 0.430210325047801
TGG 0.397705544933078
CGA 0.478059273422562
GAG 1
GGT 0.394837476099426
ACT 0.430210325047801
CTT 0.239005736137667
GTA 0.0956309751434034
GGG 0.0917782026768642
AGT 0.169216061185469
CGC 0.344168260038241
TTG 0.252390057361377
CCT 0.334608030592734
AGG 0.189292543021033
TCA 0.095640535372849
CTA 0.0956261950286807
CAA 0.191204588910134
GCC 0.413001912045889
GCG 0.173996175908222
TAT 0.253824091778203
TTT 0.225621414913958
TGC 0.334608030592734
ATT 0.430210325047801
TCC 0.275334608030593
ACG 0.235181644359465
GGC 0.669216061185469
CCG 0.315487571701721
GAA 0.286806883365201
GGA 0.286806883365201
CGG 0.152963671128107
AGG 0.189292543021033
GAG 1
ACC 0.309751434034417
ACA 0.286849904397706
TGG 0.397705544933078
AAG 0.713193116634799
CGT 0.478011472275335
CGG 0.152963671128107
CGC 0.344168260038241
GGC 0.669216061185469
AGC 0.286806883365201
GCT 0.573613766730402
GTA 0.0956309751434034
GCG 0.173996175908222
GAC 0.669216061185469
CAG 0.443594646271511
GGG 0.0917782026768642
TCG 0.221797323135755
AAC 0.573613766730402
CCA 0.239039196940727
TCA 0.095640535372849
TCT 0.382409177820268
GTT 0.286806883365201
AAG 0.713193116634799
AGA 0.1434034416826
TTG 0.252390057361377
GCA 0.09565965583174
TCG 0.221797323135755
GAA 0.286806883365201
CAC 0.239005736137667
ACT 0.430210325047801
AAA 0.286806883365201
CAT 0.141013384321224
TTT 0.225621414913958
ATA 0.0956453154875717
ATC 0.309751434034417
GTC 0.206500956022945
GGA 0.286806883365201
CCG 0.315487571701721
GAC 0.669216061185469
GTG 0.365200764818356
GCC 0.413001912045889

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