Man pages for oacar/synal
Synteny Alignment and Analysis for Saccharomyces sensu stricto
| aaTranslation | AminoAcid translation of the DNAStringSet object |
| align | Gets DNAStringSet aligns it |
| alignAnalyze | This will be THE function for alignment-analysis output |
| alignWoSmorf | Align syntenic blocks This function take align syntenic... |
| analyze | Analyze msa This function reads all output files previously... |
| analyzePairwise | Analyze pairwise alignment this is helper function for... |
| calc_identity | calculate identity |
| calcIdentity | Calculate Only Gaps are treated as difference if one sequence... |
| checkAlignment | Check if all codons are same |
| checkCodon | Check aminoacid character |
| checkFrame | this function finds correct frame sequences of intersection... |
| checkORF | Check Orf |
| countFrameShifting | Count frameshifts with MACSE |
| findBestOverlap | Finds best overlapping ORF in terms of the number of... |
| findHomolog | This function compares all overlapping ORFs with the Scer ORF... |
| findI | Find all start codons |
| findM | Find all start codons |
| findOverlappingOrfs | Finds all overlapping ORFs |
| findX | Find all stop codons |
| findYGeneSeq | Finds annotated ORF sequence from annotated sequence file... |
| macseAdjustment | Correct macse Changes some macse spesific characters for the... |
| map_alignment_sequence | map two sequences |
| readFiles | Read syntetic block sequence files |
| regSeq | Add gaps to sequence Search sequence with any number of gaps... |
| scerAnnotatedSequences | Saccharomyces Cerevisiae annotated sequence data |
| speciesVector | This function check a set of strings to create a species... |
| startCodon | Start Codon alignment |
| stopCodon | Stop codon alignment |
| subalignment | Export subalingment of the region between start and stop Scer... |
| synal_cpp-package | A short title line describing what the package does |
| turnWoGaps | Remove gaps (\'-\') |
