allOrfs |
Get ORFs from a sequence |
assemble |
Create a sequence by gathering parts a sequence |
AtoR |
Conversion of addresses |
AtoT |
Conversion of addresses |
compoSeq |
Composition in mono, di or trinucleotides of a sequence |
concat |
Concatenate two sequences into a third one |
dnaToRna |
Transformation from T to U in a sequence, and the reverse |
exactWord |
Look for motifs in a sequence |
fastaDescription |
Read the description field from a fasta file |
freeAllSeq |
Free all sequences |
freeSeq |
Free one sequence |
GeneR |
Overview of GeneR package |
getAccn |
Return globals variables of a sequence |
getBegSeq |
Return globals variables of a sequence |
getEndSeq |
Return globals variables of a sequence |
getParam |
Give global variables associated to a sequence |
getSeq |
Extract regions from a sequence |
getSeqSize |
Return globals variables of a sequence |
getStrand |
Return globals variables of a sequence |
globals |
Globals variables on Gene sequences |
indexEmbl |
Create an index for a fasta,embl,gbk file |
indexFasta |
Create an index for a fasta,embl,gbk file |
indexGbk |
Create an index for a fasta,embl,gbk file |
insertSeq |
Insert a sequence in another sequence |
makeIndex |
Make an index for a bank file |
maxOrf |
Get ORFs from a sequence |
multiExtract |
Extract regions from a sequence |
paramFromIndex |
Extract parameters from an index file |
placeString |
Put a character string into a sequence buffer. |
posMaskedSeq |
Get all masked regions |
readEmbl |
Read a sequence from a Fasta, Embl or GeneBank file. |
readEmblLocation |
Get features from a GeneBank file |
readFasta |
Read a sequence from a Fasta, Embl or GeneBank file. |
readGbk |
Read a sequence from a Fasta, Embl or GeneBank file. |
readGbkLocation |
Get features from a GeneBank file |
readSeq |
Read a sequence from a Fasta, Embl or GeneBank file. |
revComp |
Performs the reverse of a sequence |
rnaToDna |
Transformation from T to U in a sequence, and the reverse |
RtoA |
Conversion of addresses |
RtoT |
Conversion of addresses |
seqNcbi |
Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs |
seqSize |
Size of all sequence buffers |
seqUrl |
Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs |
setAccn |
Set globals variables of a sequence |
setBegSeq |
Set globals variables of a sequence |
setEndSeq |
Set globals variables of a sequence |
setParam |
Set global variables associated to a sequence |
setSeqSize |
Set globals variables of a sequence |
setStrand |
Set globals variables of a sequence |
showTable |
Translation from DNA trinucleotides to proteine |
sizeSeq |
Size of a sequence in a bufseq |
sizeSeqEmbl |
Size of a sequence from a fasta/embl/gbk file |
sizeSeqFasta |
Size of a sequence from a fasta/embl/gbk file |
sizeSeqGbk |
Size of a sequence from a fasta/embl/gbk file |
str2ascii |
Convert a string in its ascii code |
strComp |
Performs the reverse of a sequence |
strCompoSeq |
Composition in mono, di or trinucleotides of a sequence |
strMultiExtract |
Extract regions from a sequence |
strReadEmbl |
Read a sequence from a Fasta, Embl or GeneBank file. |
strReadFasta |
Read a sequence from a Fasta, Embl or GeneBank file. |
strReadGbk |
Read a sequence from a Fasta, Embl or GeneBank file. |
strTranslate |
Translation from DNA trinucleotides to proteine |
translate |
Translation from DNA trinucleotides to proteine |
TtoA |
Conversion of addresses |
TtoR |
Conversion of addresses |
writeEmblComment |
Write to Embl file |
writeEmblLine |
Write to Embl file |
writeEmblSeq |
Write to Embl file |
writeFasta |
Write sequences into fasta file format |