Man pages for oacar/synal
Synteny Alignment and Analysis for Saccharomyces sensu stricto

aaTranslationAminoAcid translation of the DNAStringSet object
alignWoSmorfAlign syntenic blocks This function take align syntenic...
calcIdentityCalculate Only Gaps are treated as difference if one sequence...
checkAlignmentCheck if all codons are same
checkCodonCheck aminoacid character
checkORFCheck Orf
countFrameShiftingCount frameshifts with MACSE
findBothSearch for both start and stop codons to get the overlapping...
findCodonfind Codon Searches for start or stop codons For start codon...
findMFind all start codons
findNextStopSearch for stop codon to get the overlapping orf
findORFFind orf start and stop coordinates
findPrevStartSearch for start codon to get the overlapping orf
findSmallFrameFind small ORF frame Finds the ORF region over the other...
findXFind all stop codons
macseAdjustmentCorrect macse Changes some macse spesific characters for the...
readFilesRead syntetic block sequence files
regSeqAdd gaps to sequence Search sequence with any number of gaps...
startCodonStart Codon alignment
stopCodonStop codon alignment
subalignmentExport subalingment of the region between start and stop Scer...
turnWoGapsRemove gaps (\'-\')
oacar/synal documentation built on July 20, 2018, 12:24 a.m.