CMA: CMA: **C**orrelated **M**utation **A**nalysis An R package...

In etaijacob/CMA: An R package for correlated mutation analysis using both codon and amino acid levels

Description

CMA: **C**orrelated **M**utation **A**nalysis An R package for correlated mutation analysis using both codon and amino acid levels

Details

CMA provides several methods for calculating correlated mutations analysis. Methods that are currently provided in this package are: OMES, MI, DCA.

If you use this package please cite:

Etai Jacob, Ron Unger and Amnon Horovitz (2015). Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis. eLife 2015;10.7554/eLife.08932 URL http://dx.doi.org/10.7554/eLife.08932.

It has several functions for correlated mutation analysis:

• Correlated mutation analysis at the codon and amino acid levels

• Read fasta and stockholm format files

To learn more about CMA, start with the vignettes: browseVignettes(package = "CMA")

See Also

PDBs2Pfam if you want to calculate the accuracy of your predictions based on solved structures.

https://github.com/etaijacob/AA2CODON if you want to generate the input files

Some notes about MSA characters and their use:

HMM models often contain dots (".") and lower-case letters, which are preserved in the aligned-alignment view. Alignment columns with dots or lower-case letters are not present in the HMM profile (see the Pfam FAQ). Thus, an HMM profile can contain less columns than its seed alignment. From PFAM FAQ http://pfam.xfam.org/help#tabview=tab3 The '-' and '.' characters both represent gap characters. However they do tell you some extra information about how the HMM has generated the alignment. The '-' symbols are where the alignment of the sequence has used a delete state in the HMM to jump past a match state. This means that the sequence is missing a column that the HMM was expecting to be there. The '.' character is used to pad gaps where one sequence in the alignment has sequence from the HMMs insert state. See the alignment below where both characters are used. The HMM states emitting each column are shown. Note that residues emitted from the Insert (I) state are in lower case.

FLPA_METMA/1-193 —MPEIRQLSEGIFEVTKD.KKQLSTLNLDPGKVVYGEKLISVEGDE

FBRL_XENLA/86-317 RKVIVEPHR-HEGIFICRGK.EDALVTKNLVPGESVYGEKRISVEDGE

FBRL_MOUSE/90-321 KNVMVEPHR-HEGVFICRGK.EDALFTKNLVPGESVYGEKRVSISEGD

O75259/81-312 KNVMVEPHR-HEGVFICRGK.EDALVTKNLVPGESVYGEKRVSISEGD

FBRL_SCHPO/71-303 AKVIIEPHR-HAGVFIARGK.EDLLVTRNLVPGESVYNEKRISVDSPD

O15647/71-301 GKVIVVPHR-FPGVYLLKGK.SDILVTKNLVPGESVYGEKRYEVMTED

FBRL_TETTH/64-294 KTIIVK-HR-LEGVFICKGQ.LEALVTKNFFPGESVYNEKRMSVEENG

FBRL_LEIMA/57-291 AKVIVEPHMLHPGVFISKAK.TDSLCTLNMVPGISVYGEKRIELGATQ

Q9ZSE3/38-276 SAVVVEPHKVHAGIFVSRGKsEDSLATLNLVPGVSVYGEKRVQTETTD

HMM STATES MMMMMMMMMMMMMMMMMMMMIMMMMMMMMMMMMMMMMMMMMMMMMMMM

In this program: Lower-case letters and (".") characters are filtered out, upper-case letters and "-" characters are preserved. Other characters are not allowed. Only the 20 basic IUPAC protein single-letters are allowed.

This implementation of DCA is based mainly on Andrea and Martin's MATLAB source code (See below).

Copyright for this R implementation: 2015 - Etai Jacob [e-mail]

Copyright for the matlab implementation which the DCA R source code is based on: 2011/12 - Andrea Pagnani [e-mail] and Martin Weigt [e-mail]

Further description of the DCA algorithm can be found at:

F Morcos, A Pagnani, B Lunt, A Bertolino, DS Marks, C Sander, R Zecchina, JN Onuchic, T Hwa, M Weigt (2011), Direct-coupling analysis of residue co-evolution captures native contacts across many protein families, Proc. Natl. Acad. Sci. 108:E1293-1301.

etaijacob/CMA documentation built on Dec. 27, 2019, 4:17 p.m.