predict-methods: Predict oligomerization of one or more coiled coil segments
In procoil: Prediction of Oligomerization of Coiled Coil Proteins

Description Usage Arguments Details Value Author(s) References See Also Examples

Function for predicting the oligomerization of one or multiple coiled coil segments

1 2	## S4 method for signature 'CCModel' predict(object, seq, reg)

`object`	The model to be considered; can either be one of the models included in the package (`PrOCoilModel` and `PrOCoilModelBA`) or any other model loaded or created by the user. For a detailed explanation of the two default models, see `CCModel`.
`seq`	One or several amino acid sequences; valid characters are all uppercase letters except ‘B’, ‘J’, ‘O’, ‘U’, ‘X’, and ‘Z’; invalid characters are tolerated, but ignored by the prediction. This argument can be a character vector, an `AAString` object, an `AAStringSet` object, or an `AAVector` object
`reg`	a character vector containing the heptad register(s); valid characters are the lowercase letters ‘a’-‘g’ and dashes ‘-’. Can also be omitted, see details below.

The function predict is the most important one in the procoil package. It is used to apply a coiled coil prediction model to coiled coil sequences/segments. It uses the discriminant function described in CCModel. By default the final classification is computed on the basis of the discriminant function value f(x). If f(x)>=0, the sequence x is predicted as trimer, otherwise as dimer.

If the reg argument is missing, predict looks whether the object passed as argument seq includes heptad register information, either as an attribute reg (if seq is a character vector), as metadata field reg (if seq is an AAString or AAStringSet object), or via annotation metadata (if seq is an AAStringSet or AAVector object; see annotationMetadata). In any case, the reg argument has priority over all other ways of specifying the heptad annotation. In other words, if reg is specified and seq contains heptad annotations in one of the ways described above, the reg argument has priority and the heptad annotation in seq is ignored.

The reg argument must have exactly as many elements as seq has sequences, and the registers must be aligned to the sequences, i.e. the first register must be exactly as long as the first sequence, and so on.

If heptad registers contain dashes, the predict function extracts all contiguous coiled coil segments and computes predictions for all of them. The returned CCProfile object then contains profiles/predictions of all coiled coil segments that were extracted from seq (see example below).

returns a CCProfile object

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

http://www.bioinf.jku.at/software/procoil/

Mahrenholz, C.C., Abfalter, I.G., Bodenhofer, U., Volkmer, R., and Hochreiter, S. (2011) Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics 10(5):M110.004994. DOI: 10.1074/mcp.M110.004994

procoil, CCModel, CCProfile

## predict oligomerization of GCN4 wildtype
GCN4wt <- predict(PrOCoilModel,
                  "MKQLEDKVEELLSKNYHLENEVARLKKLV",
                  "abcdefgabcdefgabcdefgabcdefga")

## show result
GCN4wt

## example with four GCN4 mutations
GCN4mSeq <- c("GCN4wt"        ="MKQLEDKVEELLSKNYHLENEVARLKKLV",
              "GCN4_N16Y_L19T"="MKQLEDKVEELLSKYYHTENEVARLKKLV",
              "GCN4_E22R_K27E"="MKQLEDKVEELLSKNYHLENRVARLEKLV",
              "GCN4_V23K_K27E"="MKQLEDKVEELLSKNYHLENEKARLEKLV")

## to illustrate the alternative interface, we convert this
## character vector to an 'AAStringSet' object and add
## heptad registers as annotation metadata
GCN4mAA <- AAStringSet(GCN4mSeq)
annotationMetadata(GCN4mAA, annCharset="abcdefg") <-
    rep("abcdefgabcdefgabcdefgabcdefga", 4)

## predict oligomerization (note: no 'reg' argument!)
GCN4mut <- predict(PrOCoilModel, GCN4mAA)

## display summary of result
GCN4mut

## predict oligomerization of unknown sequence (Marcoil example)
MarcoilEx <- predict(PrOCoilModel,
   "MGECDQLLVFMITSRVLVLSTLIIMDSRQVYLENLRQFAENLRQNIENVHSFLENLRADLENLRQKFPGKWYSAMPGRHG",
   "-------------------------------abcdefgabcdefgabcdefgabcdefgabcdefg--------------")

## show results
MarcoilEx