| SA | Bio.Alignment.Soap |
| SAM | Bio.Alignment.Soap |
| sameRead | Bio.Alignment.Bowtie |
| score |
| 1 (Function) | Bio.Alignment.BED |
| 2 (Function) | Bio.GFF3.Feature |
| Selector | Bio.Alignment.AlignData |
| Seq | Bio.Sequence.SeqData, Bio.Sequence |
| SeqData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence |
| seqData |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| 3 (Function) | Bio.Location.SeqLocation |
| 4 (Function) | Bio.GFF3.FeatureHierSequences |
| seqdata | Bio.Sequence.SeqData, Bio.Sequence |
| seqDataPadded |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| seqheader | Bio.Sequence.SeqData, Bio.Sequence |
| SeqId | Bio.Alignment.BlastData |
| seqid | Bio.GFF3.Feature |
| seqlabel | Bio.Sequence.SeqData, Bio.Sequence |
| seqlength | Bio.Sequence.SeqData, Bio.Sequence |
| SeqLoc | Bio.Location.SeqLocation |
| seqLoc | Bio.GFF3.Feature |
| SeqLocMap | Bio.Location.SeqLocMap |
| seqmap | Bio.Sequence.SeqData, Bio.Sequence |
| SeqName | Bio.Location.OnSeq |
| seqNt | Bio.Location.Position |
| seqNtPadded | Bio.Location.Position |
| SeqPos | Bio.Location.SeqLocation |
| seqqual | Bio.Sequence.SeqData, Bio.Sequence |
| seqToStr | Bio.Sequence.SeqData |
| sequ |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| Sequence | Bio.Sequence.SeqData, Bio.Sequence |
| sequence' | Bio.Util |
| sequences | Bio.GFF3.FeatureHierSequences |
| Ser | Bio.Sequence.SeqData, Bio.Sequence |
| setHeader | Bio.Sequence.SeqData, Bio.Sequence |
| SFF |
| 1 (Type/Class) | Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF |
| sffToSequence | Bio.Sequence.SFF |
| Shape | Bio.Sequence.HashWord |
| showalign | Bio.Alignment.AlignData |
| showT | Bio.Util.TestBase |
| sigint | Bio.Sequence.SFF_filters |
| simpleMx | Bio.Alignment.Matrices |
| slength |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| slide |
| 1 (Function) | Bio.Location.Position |
| 2 (Function) | Bio.Location.ContigLocation |
| small | Bio.Sequence.AminoProperties |
| SoapAlign | Bio.Alignment.Soap |
| SoapAlignMismatch | Bio.Alignment.Soap |
| sortExons | Bio.GFF3.SGD |
| source | Bio.GFF3.Feature |
| splitWhen | Bio.Util |
| start | Bio.GFF3.Feature |
| startPos |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| STP | Bio.Sequence.SeqData, Bio.Sequence |
| Strand |
| 1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| 2 (Type/Class) | Bio.Location.Strand |
| strand |
| 1 (Function) | Bio.Alignment.PSL |
| 2 (Function) | Bio.Location.Position |
| 3 (Function) | Bio.Location.ContigLocation |
| 4 (Function) | Bio.Alignment.Bowtie |
| 5 (Function) | Bio.Alignment.Soap |
| 6 (Function) | Bio.Alignment.BED |
| 7 (Function) | Bio.GFF3.Feature |
| Stranded | Bio.Location.Strand |
| stranded | Bio.Location.Strand |
| strandP | Bio.Sequence.AminoProperties |
| Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| subject |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| SubstMx | Bio.Alignment.AlignData |
