! | Bio.Sequence.SeqData, Bio.Sequence |
? | Bio.Sequence.SeqData |
Ala | Bio.Sequence.SeqData, Bio.Sequence |
Alignment | Bio.Alignment.AlignData |
Amino | Bio.Sequence.SeqData, Bio.Sequence |
Ann | Bio.Sequence.GOA |
Annotation | Bio.Sequence.GOA |
Arg | Bio.Sequence.SeqData, Bio.Sequence |
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 |
Aux | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
aux |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
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 |
Branch | Bio.Clustering |
Chr | Bio.Alignment.AlignData |
Clustered | Bio.Clustering |
cluster_sl | Bio.Clustering |
columns | Bio.Alignment.AlignData |
Comp | Bio.Sequence.GOA |
compact | Bio.Sequence.HashWord |
compl | Bio.Sequence.SeqData, Bio.Sequence |
complement | Bio.Sequence.HashWord |
contig | Bio.Alignment.ACE |
contigous | Bio.Sequence.HashWord, Bio.Sequence |
countIO | Bio.Util |
countSeqs | Bio.Sequence.Fasta |
Cys | Bio.Sequence.SeqData, Bio.Sequence |
database | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
dbchars | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
dbsequences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
decode2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
decomment | Bio.Sequence.GOA |
Del | Bio.Alignment.AlignData |
Dir | Bio.Alignment.AlignData |
Edit | Bio.Alignment.AlignData |
EditList | Bio.Alignment.AlignData |
entropy | Bio.Sequence.Entropy, Bio.Sequence |
eval | Bio.Alignment.AlignData |
EvidenceCode | Bio.Sequence.GOA |
extractGaps | Bio.Alignment.AlignData |
e_val |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
flatten | Bio.Alignment.BlastFlat |
fragments | Bio.Alignment.ACE |
Frame | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
fromIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
fromStr | Bio.Sequence.SeqData, Bio.Sequence |
Func | Bio.Sequence.GOA |
Fwd | Bio.Alignment.AlignData |
gapped | Bio.Sequence.HashWord |
Gaps | Bio.Alignment.AlignData |
genkeys | Bio.Sequence.HashWord |
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.GOA |
GoClass | Bio.Sequence.GOA |
GoDef |
1 (Type/Class) | Bio.Sequence.GOA |
2 (Data Constructor) | Bio.Sequence.GOA |
GoTerm | Bio.Sequence.GOA |
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 |
hReadPhd | Bio.Sequence.Phd, Bio.Sequence |
hWriteFasta | Bio.Sequence.Fasta, Bio.Sequence |
hWriteFastaQual | Bio.Sequence.Fasta, 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.GOA |
IDA | Bio.Sequence.GOA |
identity |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
IEA | Bio.Sequence.GOA |
IEP | Bio.Sequence.GOA |
IGC | Bio.Sequence.GOA |
IGI | Bio.Sequence.GOA |
Ile | Bio.Sequence.SeqData, Bio.Sequence |
IMP | Bio.Sequence.GOA |
indirect | Bio.Alignment.Multiple |
Ins | Bio.Alignment.AlignData |
insertGaps | Bio.Alignment.AlignData |
IPI | Bio.Sequence.GOA |
isCurated | Bio.Sequence.GOA |
isN | Bio.Sequence.HashWord |
isRepl | Bio.Alignment.AlignData |
ISS | Bio.Sequence.GOA |
k2n | Bio.Sequence.HashWord |
k2n' | Bio.Sequence.HashWord |
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 |
Leu | Bio.Sequence.SeqData, Bio.Sequence |
lines | Bio.Util |
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 |
Lys | Bio.Sequence.SeqData, Bio.Sequence |
matches | Bio.Alignment.BlastData |
Met | Bio.Sequence.SeqData, Bio.Sequence |
Minus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
mkAnn | Bio.Sequence.GOA |
mkGoDef | Bio.Sequence.GOA |
mkSeqs | Bio.Sequence.Fasta |
mylines | Bio.Util |
n2i' | Bio.Sequence.HashWord |
n2k | Bio.Sequence.HashWord |
NAS | Bio.Sequence.GOA |
ND | Bio.Sequence.GOA |
NR | Bio.Sequence.GOA |
Offset | Bio.Sequence.SeqData, Bio.Sequence |
on | Bio.Alignment.AlignData |
pam30 | Bio.Alignment.Matrices |
pam70 | Bio.Alignment.Matrices |
parse | Bio.Alignment.Blast |
Phe | Bio.Sequence.SeqData, Bio.Sequence |
Plus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Pro | Bio.Sequence.SeqData, Bio.Sequence |
Proc | Bio.Sequence.GOA |
progressive | Bio.Alignment.Multiple |
ptest | Bio.Alignment.ACE |
qlength |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
Qual | Bio.Sequence.SeqData, Bio.Sequence |
QualData | Bio.Sequence.SeqData, Bio.Sequence |
qualMx | Bio.Alignment.QAlign |
query |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
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.GOA |
rcontig | Bio.Sequence.HashWord, Bio.Sequence |
rcpacked | Bio.Sequence.HashWord, Bio.Sequence |
read2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
readACE | Bio.Alignment.ACE |
readFasta | Bio.Sequence.Fasta, Bio.Sequence |
readFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
readGO | Bio.Sequence.GOA |
readGOA | Bio.Sequence.GOA |
readPhd | Bio.Sequence.Phd, Bio.Sequence |
readQual | Bio.Sequence.Fasta, Bio.Sequence |
reads | Bio.Alignment.ACE |
readXML | Bio.Alignment.BlastXML |
Repl | Bio.Alignment.AlignData |
results | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Rev | Bio.Alignment.AlignData |
revcompl | Bio.Sequence.SeqData, Bio.Sequence |
Selector | Bio.Alignment.AlignData |
Seq | Bio.Sequence.SeqData, Bio.Sequence |
SeqData | Bio.Sequence.SeqData, Bio.Sequence |
seqdata | Bio.Sequence.SeqData, Bio.Sequence |
seqheader | Bio.Sequence.SeqData, Bio.Sequence |
SeqId | Bio.Alignment.BlastData |
seqlabel | Bio.Sequence.SeqData, Bio.Sequence |
seqlength | Bio.Sequence.SeqData, Bio.Sequence |
seqqual | Bio.Sequence.SeqData, Bio.Sequence |
Sequence | Bio.Sequence.SeqData, Bio.Sequence |
sequence' | Bio.Util |
Ser | Bio.Sequence.SeqData, Bio.Sequence |
Shape | Bio.Sequence.HashWord |
showalign | Bio.Alignment.AlignData |
simpleMx | Bio.Alignment.Matrices |
slength |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
splitWhen | Bio.Util |
STP | Bio.Sequence.SeqData, Bio.Sequence |
Strand | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
subject |
1 (Function) | Bio.Alignment.BlastData |
2 (Function) | Bio.Alignment.BlastFlat |
SubstMx | Bio.Alignment.AlignData |
TAS | Bio.Sequence.GOA |
Thr | Bio.Sequence.SeqData, Bio.Sequence |
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 |
UniProtAcc | Bio.Sequence.GOA |
unval | Bio.Sequence.HashWord |
Val | Bio.Sequence.SeqData, Bio.Sequence |
val | Bio.Sequence.HashWord |
writeACE | Bio.Alignment.ACE |
writeFasta | Bio.Sequence.Fasta, Bio.Sequence |
writeFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
writeQual | Bio.Sequence.Fasta, Bio.Sequence |
Xaa | Bio.Sequence.SeqData, Bio.Sequence |
Xle | Bio.Sequence.SeqData, Bio.Sequence |