! | Bio.Sequence.SeqData, Bio.Sequence |
? | Bio.Sequence.SeqData |
Ala | Bio.Sequence.SeqData, Bio.Sequence |
Align |
1 (Type/Class) | Bio.Alignment.Bowtie |
2 (Data Constructor) | Bio.Alignment.Bowtie |
Alignment | Bio.Alignment.AlignData |
Amino | Bio.Sequence.SeqData, Bio.Sequence |
andSameSeq | Bio.Location.OnSeq |
Ann | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Annotation | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
appendHeader | Bio.Sequence.SeqData, Bio.Sequence |
Arg | Bio.Sequence.SeqData, Bio.Sequence |
asksGFF | Bio.GFF3.FeatureHierSequences |
Asm | Bio.Alignment.ACE |
Asn | Bio.Sequence.SeqData, Bio.Sequence |
Asp | Bio.Sequence.SeqData, Bio.Sequence |
Assembly | Bio.Alignment.ACE |
Asx | Bio.Sequence.SeqData, Bio.Sequence |
attrByTag | Bio.GFF3.Feature |
attributes | Bio.GFF3.Feature |
attrTag | Bio.GFF3.Feature |
attrValues | Bio.GFF3.Feature |
Aux | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
aux |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
b36 | Bio.Sequence.SFF_name |
bases | Bio.Sequence.SFF |
bits |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
blastdate | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
BlastFlat |
1 (Type/Class) | Bio.Alignment.BlastFlat |
2 (Data Constructor) | Bio.Alignment.BlastFlat |
BlastHit |
1 (Type/Class) | Bio.Alignment.BlastData |
2 (Data Constructor) | Bio.Alignment.BlastData |
BlastMatch |
1 (Type/Class) | Bio.Alignment.BlastData |
2 (Data Constructor) | Bio.Alignment.BlastData |
blastn_default | Bio.Alignment.Matrices |
blastprogram | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
BlastRecord |
1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
2 (Data Constructor) | Bio.Alignment.BlastData |
blastreferences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
BlastResult |
1 (Type/Class) | Bio.Alignment.BlastData |
2 (Data Constructor) | Bio.Alignment.BlastData |
blastversion | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
blosum45 | Bio.Alignment.Matrices |
blosum62 | Bio.Alignment.Matrices |
blosum80 | Bio.Alignment.Matrices |
bounds |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
Branch | Bio.Clustering |
castToAmino | Bio.Sequence.SeqData, Bio.Sequence |
castToNuc | Bio.Sequence.SeqData, Bio.Sequence |
checkInvariants |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.GFF3.FeatureHier |
children |
1 (Function) | Bio.GFF3.FeatureHier |
2 (Function) | Bio.GFF3.FeatureHierSequences |
childrenM | Bio.GFF3.FeatureHier |
Chr | Bio.Alignment.AlignData |
chromosomes | Bio.GFF3.SGD |
clip_adapter_left | Bio.Sequence.SFF |
clip_adapter_right | Bio.Sequence.SFF |
clip_qual_left | Bio.Sequence.SFF |
clip_qual_right | Bio.Sequence.SFF |
Clustered | Bio.Clustering |
cluster_sl | Bio.Clustering |
columns | Bio.Alignment.AlignData |
CommonHeader |
1 (Type/Class) | Bio.Sequence.SFF |
2 (Data Constructor) | Bio.Sequence.SFF |
Comp | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
compact | Bio.Sequence.HashWord |
compl | Bio.Sequence.SeqData, Bio.Sequence |
complement | Bio.Sequence.HashWord |
contig | Bio.Alignment.ACE |
ContigLoc |
1 (Type/Class) | Bio.Location.ContigLocation |
2 (Data Constructor) | Bio.Location.ContigLocation |
contigLoc | Bio.GFF3.Feature |
contigous | Bio.Sequence.HashWord, Bio.Sequence |
ContigSeqLoc | Bio.Location.SeqLocation |
convert | Bio.Sequence.SFF |
countIO | Bio.Util |
countSeqs | Bio.Sequence.Fasta |
Cys | Bio.Sequence.SeqData, Bio.Sequence |
database | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
date | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
dbchars | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
dbsequences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
decCh | Bio.Sequence.SFF_name |
decode2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
decode36 | Bio.Sequence.SFF_name |
decodeDate | Bio.Sequence.SFF_name |
decodeKO | Bio.Sequence.KEGG |
decodeLocation | Bio.Sequence.SFF_name |
decodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
decodeUP | Bio.Sequence.KEGG |
decomment | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
defragSeq | Bio.Sequence.SeqData |
Del | Bio.Alignment.AlignData |
delete |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.GFF3.FeatureHier |
deleteBy | Bio.Location.LocMap |
Dir | Bio.Alignment.AlignData |
display |
1 (Function) | Bio.Location.Position |
2 (Function) | Bio.Location.ContigLocation |
3 (Function) | Bio.Location.Location |
4 (Function) | Bio.Location.SeqLocation |
displayContigSeqLoc | Bio.Location.SeqLocation |
displaySeqPos | Bio.Location.SeqLocation |
divMods | Bio.Sequence.SFF_name |
E | Bio.Util.TestBase |
Edit | Bio.Alignment.AlignData |
EditList | Bio.Alignment.AlignData |
EL | Bio.Util.TestBase |
empty | Bio.Location.SeqLocMap |
encode2Bit | Bio.Sequence.TwoBit |
encode36 | Bio.Sequence.SFF_name |
encodeDate | Bio.Sequence.SFF_name |
encodeLocation | Bio.Sequence.SFF_name |
encodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
encodeRegion | Bio.Sequence.SFF_name |
end | Bio.GFF3.Feature |
endPos |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
entropy | Bio.Sequence.Entropy, Bio.Sequence |
Eq | Bio.Util.TestBase |
ES | Bio.Util.TestBase |
escapeAllBut | Bio.GFF3.Escape |
escapeAllOf | Bio.GFF3.Escape |
escapeByteString | Bio.GFF3.Escape |
ESet | Bio.Util.TestBase |
EST | Bio.Util.TestBase |
ESTq | Bio.Util.TestBase |
EST_long | Bio.Util.TestBase |
EST_set | Bio.Util.TestBase |
EST_short | Bio.Util.TestBase |
eval | Bio.Alignment.AlignData |
EvidenceCode | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
extend |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
extractGaps | Bio.Alignment.AlignData |
e_val |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
Feature |
1 (Type/Class) | Bio.GFF3.Feature |
2 (Data Constructor) | Bio.GFF3.Feature |
FeatureHier | Bio.GFF3.FeatureHier |
FeatureHierSequences | Bio.GFF3.FeatureHierSequences |
features |
1 (Function) | Bio.GFF3.FeatureHier |
2 (Function) | Bio.GFF3.FeatureHierSequences |
featureSequence | Bio.GFF3.FeatureHierSequences |
flatten | Bio.Alignment.BlastFlat |
Flow | Bio.Sequence.SFF |
flow | Bio.Sequence.SFF |
flowgram | Bio.Sequence.SFF |
flowgram_fmt | Bio.Sequence.SFF |
flow_index | Bio.Sequence.SFF |
flow_length | Bio.Sequence.SFF |
fragments | Bio.Alignment.ACE |
Frame | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
fromIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
fromList |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.Location.SeqLocMap |
3 (Function) | Bio.GFF3.FeatureHier |
fromLists | Bio.GFF3.FeatureHierSequences |
fromN | Bio.Util.TestBase |
fromPosLen | Bio.Location.ContigLocation |
fromQ | Bio.Util.TestBase |
fromStartEnd | Bio.Location.ContigLocation |
fromStr | Bio.Sequence.SeqData, Bio.Sequence |
ftype | Bio.GFF3.Feature |
Func | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Fwd |
1 (Data Constructor) | Bio.Alignment.AlignData |
2 (Data Constructor) | Bio.Location.Strand |
gapped | Bio.Sequence.HashWord |
Gaps | Bio.Alignment.AlignData |
geneCDSes | Bio.GFF3.SGD |
geneCDS_SLM | Bio.GFF3.SGD |
genes | Bio.GFF3.SGD |
geneSeqLoc | Bio.GFF3.SGD |
geneSequence | Bio.GFF3.SGD |
genkeys | Bio.Sequence.HashWord |
genNonNegOffset | Bio.Util.TestBase |
genOffset | Bio.Util.TestBase |
genPositiveOffset | Bio.Util.TestBase |
genReadKegg | Bio.Sequence.KEGG |
getSequence | Bio.GFF3.FeatureHierSequences |
GFFAttr |
1 (Type/Class) | Bio.GFF3.Feature |
2 (Data Constructor) | Bio.GFF3.Feature |
Gln | Bio.Sequence.SeqData, Bio.Sequence |
global_align |
1 (Function) | Bio.Alignment.SAlign |
2 (Function) | Bio.Alignment.AAlign |
3 (Function) | Bio.Alignment.QAlign |
global_score |
1 (Function) | Bio.Alignment.SAlign |
2 (Function) | Bio.Alignment.AAlign |
3 (Function) | Bio.Alignment.QAlign |
Glu | Bio.Sequence.SeqData, Bio.Sequence |
Glx | Bio.Sequence.SeqData, Bio.Sequence |
Gly | Bio.Sequence.SeqData, Bio.Sequence |
GO | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
GoClass | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
GoDef |
1 (Type/Class) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
2 (Data Constructor) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
GoHierarchy | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
GoTerm | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
group | Bio.Alignment.Soap |
hash | Bio.Sequence.HashWord, Bio.Sequence |
hashes | Bio.Sequence.HashWord, Bio.Sequence |
HashF | Bio.Sequence.HashWord, Bio.Sequence |
hasqual | Bio.Sequence.SeqData |
HF | Bio.Sequence.HashWord, Bio.Sequence |
His | Bio.Sequence.SeqData, Bio.Sequence |
hits | Bio.Alignment.BlastData |
hRead2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
hReadFasta | Bio.Sequence.Fasta, Bio.Sequence |
hReadFastQ | Bio.Sequence.FastQ, Bio.Sequence |
hReadPhd | Bio.Sequence.Phd, Bio.Sequence |
hWrite2Bit | Bio.Sequence.TwoBit |
hWriteFasta | Bio.Sequence.Fasta, Bio.Sequence |
hWriteFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
hWriteFastQ | Bio.Sequence.FastQ, Bio.Sequence |
hWriteQual | Bio.Sequence.Fasta, Bio.Sequence |
h_from |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
h_to |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
IC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
IDA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
identity |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
ids | Bio.GFF3.Feature |
IEA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
IEP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
IGC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
IGI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Ile | Bio.Sequence.SeqData, Bio.Sequence |
IMP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Index | Bio.Sequence.SFF |
index_length | Bio.Sequence.SFF |
index_offset | Bio.Sequence.SFF |
indirect | Bio.Alignment.Multiple |
Ins | Bio.Alignment.AlignData |
insert |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.Location.SeqLocMap |
3 (Function) | Bio.GFF3.FeatureHier |
insertGaps | Bio.Alignment.AlignData |
integralRandomR | Bio.Util.TestBase |
IPI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
isCurated | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
isN | Bio.Sequence.HashWord |
isRepl | Bio.Alignment.AlignData |
ISS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
isWithin |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
3 (Function) | Bio.Location.SeqLocation |
k2n | Bio.Sequence.HashWord |
k2n' | Bio.Sequence.HashWord |
key | Bio.Sequence.SFF |
key_length | Bio.Sequence.SFF |
KO |
1 (Type/Class) | Bio.Sequence.KEGG |
2 (Data Constructor) | Bio.Sequence.KEGG |
ksort | Bio.Sequence.HashWord, Bio.Sequence |
KWords | Bio.Sequence.Entropy, Bio.Sequence |
kwords | Bio.Sequence.Entropy, Bio.Sequence |
lazyMany | Bio.Util.Parsex |
Leaf | Bio.Clustering |
leftoffset | Bio.Alignment.Bowtie |
length |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
3 (Function) | Bio.Alignment.Bowtie |
4 (Function) | Bio.Alignment.Soap |
5 (Function) | Bio.GFF3.Feature |
Leu | Bio.Sequence.SeqData, Bio.Sequence |
lines | Bio.Util |
Loc |
1 (Type/Class) | Bio.Location.Location |
2 (Data Constructor) | Bio.Location.Location |
loc | Bio.GFF3.Feature |
local_align |
1 (Function) | Bio.Alignment.SAlign |
2 (Function) | Bio.Alignment.AAlign |
3 (Function) | Bio.Alignment.QAlign |
local_score |
1 (Function) | Bio.Alignment.SAlign |
2 (Function) | Bio.Alignment.AAlign |
3 (Function) | Bio.Alignment.QAlign |
LocMap | Bio.Location.LocMap |
lookupId |
1 (Function) | Bio.GFF3.FeatureHier |
2 (Function) | Bio.GFF3.FeatureHierSequences |
lookupIdChildren | Bio.GFF3.FeatureHier |
lookupOverlaps |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.Location.SeqLocMap |
lookupWithin |
1 (Function) | Bio.Location.LocMap |
2 (Function) | Bio.Location.SeqLocMap |
Lys | Bio.Sequence.SeqData, Bio.Sequence |
matches | Bio.Alignment.BlastData |
Met | Bio.Sequence.SeqData, Bio.Sequence |
Minus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Mismatch |
1 (Type/Class) | Bio.Alignment.Bowtie |
2 (Data Constructor) | Bio.Alignment.Bowtie |
mismatches |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
mismatchSeqPos |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
mkSeqs | Bio.Sequence.Fasta |
mmoffset | Bio.Alignment.Bowtie |
mylines | Bio.Util |
N | Bio.Util.TestBase |
n2i' | Bio.Sequence.HashWord |
n2k | Bio.Sequence.HashWord |
name |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
3 (Function) | Bio.GFF3.Feature |
namedSLM | Bio.GFF3.SGD |
name_length | Bio.Sequence.SFF |
NAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
ND | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
nhit | Bio.Alignment.Soap |
nmismatch |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
noncodingExons | Bio.GFF3.SGD |
noncodingSeqLoc | Bio.GFF3.SGD |
noncodingSequence | Bio.GFF3.SGD |
NR | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Nuc | Bio.Sequence.SeqData, Bio.Sequence |
Nucleotide | Bio.Util.TestBase |
num_bases | Bio.Sequence.SFF |
num_reads | Bio.Sequence.SFF |
Offset | Bio.Sequence.SeqData, Bio.Sequence |
offset |
1 (Function) | Bio.Location.Position |
2 (Function) | Bio.Alignment.Soap |
offset5 | Bio.Location.ContigLocation |
on | Bio.Alignment.AlignData |
onSameSeq | Bio.Location.OnSeq |
OnSeq |
1 (Type/Class) | Bio.Location.OnSeq |
2 (Data Constructor) | Bio.Location.OnSeq |
onSeqName | Bio.Location.OnSeq |
onSeqObj | Bio.Location.OnSeq |
OnSeqs | Bio.Location.OnSeq |
overlaps |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
3 (Function) | Bio.Location.SeqLocation |
overlap_align | Bio.Alignment.QAlign |
overlap_score | Bio.Alignment.QAlign |
P | Bio.Util.TestBase |
pairend | Bio.Alignment.Soap |
pam30 | Bio.Alignment.Matrices |
pam70 | Bio.Alignment.Matrices |
parentIds | Bio.GFF3.Feature |
parents |
1 (Function) | Bio.GFF3.FeatureHier |
2 (Function) | Bio.GFF3.FeatureHierSequences |
parentsM | Bio.GFF3.FeatureHier |
parse |
1 (Function) | Bio.Alignment.Blast |
2 (Function) | Bio.Sequence.FastQ |
3 (Function) | Bio.Alignment.Bowtie |
4 (Function) | Bio.Alignment.Soap |
5 (Function) | Bio.GFF3.Feature |
6 (Function) | Bio.GFF3.FeatureHierSequences |
parseMismatch | Bio.Alignment.Soap |
parseWithFasta | Bio.GFF3.Feature |
perSeq | Bio.Location.OnSeq |
perSeqUpdate | Bio.Location.OnSeq |
phase | Bio.GFF3.Feature |
Phe | Bio.Sequence.SeqData, Bio.Sequence |
Plus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Pos |
1 (Type/Class) | Bio.Location.Position |
2 (Data Constructor) | Bio.Location.Position |
posInto |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
posOutof |
1 (Function) | Bio.Location.ContigLocation |
2 (Function) | Bio.Location.Location |
Pro | Bio.Sequence.SeqData, Bio.Sequence |
Proc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
progressive | Bio.Alignment.Multiple |
Protein | Bio.Util.TestBase |
ptest | Bio.Alignment.ACE |
putSeqLn | Bio.Sequence.SeqData |
Q | Bio.Util.TestBase |
qlength |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
Qual | Bio.Sequence.SeqData, Bio.Sequence.Fasta, Bio.Sequence.SFF, Bio.Sequence |
qual |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
QualData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence |
Quality | Bio.Util.TestBase |
quality | Bio.Sequence.SFF |
qualMx | Bio.Alignment.QAlign |
qualnt | Bio.Alignment.Soap |
query |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
queryQual | Bio.Alignment.Bowtie |
querySequ | Bio.Alignment.Bowtie |
q_from |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
q_to |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
RCA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
rcontig | Bio.Sequence.HashWord, Bio.Sequence |
rcpacked | Bio.Sequence.HashWord, Bio.Sequence |
read2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
readACE | Bio.Alignment.ACE |
readbase | Bio.Alignment.Bowtie |
ReadBlock |
1 (Type/Class) | Bio.Sequence.SFF |
2 (Data Constructor) | Bio.Sequence.SFF |
readFasta | Bio.Sequence.Fasta, Bio.Sequence |
readFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
readFastQ | Bio.Sequence.FastQ, Bio.Sequence |
readGO | Bio.Sequence.GOA |
readGOA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
ReadHeader |
1 (Type/Class) | Bio.Sequence.SFF |
2 (Data Constructor) | Bio.Sequence.SFF |
ReadName |
1 (Type/Class) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
2 (Data Constructor) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
readnt | Bio.Alignment.Soap |
readObo | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
readPhd | Bio.Sequence.Phd, Bio.Sequence |
readQual | Bio.Sequence.Fasta, Bio.Sequence |
reads | Bio.Alignment.ACE |
readSFF | Bio.Sequence.SFF |
readTerms | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
readXML |
1 (Function) | Bio.Alignment.BlastXML |
2 (Function) | Bio.Alignment.BlastFlat |
read_header | Bio.Sequence.SFF |
read_name | Bio.Sequence.SFF |
refbase | Bio.Alignment.Bowtie |
refCLoc | Bio.Alignment.Bowtie |
refCSeqLoc |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
refname |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
refnt | Bio.Alignment.Soap |
refSeqLoc |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
refSeqPos |
1 (Function) | Bio.Alignment.Bowtie |
2 (Function) | Bio.Alignment.Soap |
refstart | Bio.Alignment.Soap |
region | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
removePrefix | Bio.Sequence.KEGG |
Repl | Bio.Alignment.AlignData |
results | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Rev | Bio.Alignment.AlignData |
RevCompl | Bio.Location.Strand |
revCompl | Bio.Location.Strand |
revcompl | Bio.Sequence.SeqData, Bio.Sequence |
revcompl' | Bio.Sequence.SeqData, Bio.Sequence |
rRNAs | Bio.GFF3.SGD |
runGFF | Bio.GFF3.FeatureHierSequences |
runGFFIO | Bio.GFF3.FeatureHierSequences |
SA | Bio.Alignment.Soap |
SAM | Bio.Alignment.Soap |
sameRead | Bio.Alignment.Bowtie |
score | 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 |
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 |
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 |
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.Location.Position |
2 (Function) | Bio.Location.ContigLocation |
3 (Function) | Bio.Alignment.Bowtie |
4 (Function) | Bio.Alignment.Soap |
5 (Function) | Bio.GFF3.Feature |
Stranded | Bio.Location.Strand |
stranded | Bio.Location.Strand |
Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
subject |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
SubstMx | Bio.Alignment.AlignData |
T | Bio.Util.TestBase |
TAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Test | Bio.Util.TestBase |
test |
1 (Function) | Bio.Sequence.SFF |
2 (Function) | Bio.Alignment.QAlign |
Thr | Bio.Sequence.SeqData, Bio.Sequence |
time |
1 (Function) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
2 (Function) | Bio.Util.TestBase |
toIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
toStr | Bio.Sequence.SeqData, Bio.Sequence |
toStrings | Bio.Alignment.AlignData |
translate | Bio.Sequence.SeqData, Bio.Sequence |
Trp | Bio.Sequence.SeqData, Bio.Sequence |
Tyr | Bio.Sequence.SeqData, Bio.Sequence |
unEscapeByteString | Bio.GFF3.Escape |
UniProtAcc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
Unknown | Bio.Sequence.SeqData, Bio.Sequence |
unparse |
1 (Function) | Bio.Sequence.FastQ |
2 (Function) | Bio.Alignment.Soap |
3 (Function) | Bio.GFF3.Feature |
unparseMismatch | Bio.Alignment.Soap |
unval | Bio.Sequence.HashWord |
Val | Bio.Sequence.SeqData, Bio.Sequence |
val | Bio.Sequence.HashWord |
withinContigSeqLoc | Bio.Location.SeqLocation |
withNameAndSeq | Bio.Location.OnSeq |
withSeqData | Bio.Location.OnSeq |
write2Bit | Bio.Sequence.TwoBit |
writeACE | Bio.Alignment.ACE |
writeFasta | Bio.Sequence.Fasta, Bio.Sequence |
writeFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
writeFastQ | Bio.Sequence.FastQ, Bio.Sequence |
writeQual | Bio.Sequence.Fasta, Bio.Sequence |
writeSFF | Bio.Sequence.SFF |
writeSFF' | Bio.Sequence.SFF |
Xaa | Bio.Sequence.SeqData, Bio.Sequence |
Xle | Bio.Sequence.SeqData, Bio.Sequence |
x_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
y_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF |