AtoR                    Conversion of addresses
GeneR                   Overview of GeneR package
Match                   Value Matching
Xor.globalSeg           Xor for global segments
Xor.segSet              Xor for segments sets
and.globalSeg           Intersection of global segments
and.segSet              Intersection of segments
appendSeq               Appends two sequences
as.globalSeg            GlobalSeg manipulation
as.segSet               Segments Set manipulation
assemble                Concatenates parts of a sequence
bankDensityProfile      Computes density profile(s) of a bank of fasta
                        sequences
bankSummary             Computes informations on all a bank file
compoSeq                Composition in mono, di or trinucleotides of a
                        sequence
concat                  Concatenation of two sequences
deleteCR                Delete carriage return in file
densityProfile          Density profiles
dnaToRna                DNA <-> RNA sequence rewriting
exactWord               Exact matches of an oligomer
fastaDescription        Description field reading of a fasta sequence
freeSeq                 Low level functions on buffer manipulation
getAccn                 Reading of a GeneR global variable
getOrfs                 Gets ORFs from a sequence
getParam                Reading of all the GeneR global variables
getSeq                  Sequence fragments extraction
globalSeg               Class manipulating segments
globals                 Globals variables on Gene sequences
indexFasta              Index file creation for a sequences bank
insertSeq               Sequence insertion
lowerSeq                Convert upper/lower-case characters in sequence
                        fragments
makeIndex               Index file creation for a bank file (internal
                        function)
mask                    Mask regions on a sequence
not.globalSeg           Substraction of globals segments
not.segSet              Substraction of segments sets
or.globalSeg            Union of global segments
or.segSet               Union of 2 segments sets
placeString             Sequence loading in a GeneR sequence buffer.
plot.globalSeg          Plot an object of class globalSeg
posMaskedSeq            Position of masked fragments
randomSeq               Create random sequence
readEmblDescript        Read features from an Embl bank file
readGbkLocation         Get annotations of a GeneBank or an EMBL
                        sequence
readSeq                 Sequence extraction from a bank
relist                  Group segments into global segments
revComp                 Performs the reverse of a sequence
seqSkew                 compute the strand assymetries from one
                        sequence fragment
seqSrs                  Download a sequence in Fasta / Genbank / Embl
                        format from Ncbi or Srs
setAccn                 Set globals variables of a sequence
setParam                Set global variables associated to a sequence
size.globalSeg          Size.globalSeg
sizeSeq                 Size of a sequence in a buffer
sizeSeqFasta            Size of a sequence from a fasta/embl/gbk file
sliceSegment            delineate sub-segments of equal size at both
                        sides of an origin in a segment
translate               Translation from DNA trinucleotides to proteine
writeEmblLine           Write to Embl file
writeFasta              Write sequences into fasta file format
