| bio-0.4: A bioinformatics library | Contents | Index

Search:

! | 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