pairwise sequence alignment similarity simple.


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Documentation for package `pairseqsim' version 1.0.4

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A E F I L R S T misc

-- A --

AAAlignment-class "AAAlignment" result of pairwise sequence alignment.
AAAlphabet-class Class "AAAlphabet" Amino Acid Alphabet
AASequence AASequence constructor
AASequence-class "AASequence" Object representation of a protein Sequence
AASequenceList-class Class "AASequenceList" - Container

-- E --

EBLOSUM30 Amino Acid Substitution matrices
EBLOSUM35 Amino Acid Substitution matrices
EBLOSUM40 Amino Acid Substitution matrices
EBLOSUM45 Amino Acid Substitution matrices
EBLOSUM50 Amino Acid Substitution matrices
EBLOSUM55 Amino Acid Substitution matrices
EBLOSUM60 Amino Acid Substitution matrices
EBLOSUM62 Amino Acid Substitution matrices
EBLOSUM65 Amino Acid Substitution matrices
EBLOSUM70 Amino Acid Substitution matrices
EBLOSUM75 Amino Acid Substitution matrices
EBLOSUM80 Amino Acid Substitution matrices
EBLOSUM85 Amino Acid Substitution matrices
EBLOSUM90 Amino Acid Substitution matrices
EPAM10 Amino Acid Substitution matrices
EPAM100 Amino Acid Substitution matrices
EPAM110 Amino Acid Substitution matrices
EPAM120 Amino Acid Substitution matrices
EPAM130 Amino Acid Substitution matrices
EPAM140 Amino Acid Substitution matrices
EPAM150 Amino Acid Substitution matrices
EPAM160 Amino Acid Substitution matrices
EPAM170 Amino Acid Substitution matrices
EPAM180 Amino Acid Substitution matrices
EPAM190 Amino Acid Substitution matrices
EPAM20 Amino Acid Substitution matrices
EPAM200 Amino Acid Substitution matrices
EPAM210 Amino Acid Substitution matrices
EPAM220 Amino Acid Substitution matrices
EPAM230 Amino Acid Substitution matrices
EPAM240 Amino Acid Substitution matrices
EPAM250 Amino Acid Substitution matrices
EPAM260 Amino Acid Substitution matrices
EPAM270 Amino Acid Substitution matrices
EPAM280 Amino Acid Substitution matrices
EPAM290 Amino Acid Substitution matrices
EPAM30 Amino Acid Substitution matrices
EPAM300 Amino Acid Substitution matrices
EPAM310 Amino Acid Substitution matrices
EPAM320 Amino Acid Substitution matrices
EPAM330 Amino Acid Substitution matrices
EPAM340 Amino Acid Substitution matrices
EPAM350 Amino Acid Substitution matrices
EPAM360 Amino Acid Substitution matrices
EPAM370 Amino Acid Substitution matrices
EPAM380 Amino Acid Substitution matrices
EPAM390 Amino Acid Substitution matrices
EPAM40 Amino Acid Substitution matrices
EPAM400 Amino Acid Substitution matrices
EPAM410 Amino Acid Substitution matrices
EPAM420 Amino Acid Substitution matrices
EPAM430 Amino Acid Substitution matrices
EPAM440 Amino Acid Substitution matrices
EPAM450 Amino Acid Substitution matrices
EPAM460 Amino Acid Substitution matrices
EPAM470 Amino Acid Substitution matrices
EPAM480 Amino Acid Substitution matrices
EPAM490 Amino Acid Substitution matrices
EPAM50 Amino Acid Substitution matrices
EPAM500 Amino Acid Substitution matrices
EPAM60 Amino Acid Substitution matrices
EPAM70 Amino Acid Substitution matrices
EPAM80 Amino Acid Substitution matrices
EPAM90 Amino Acid Substitution matrices

-- F --

frequency,AASequence-method "AASequence" Object representation of a protein Sequence

-- I --

infogrep reader for databases in Fasta file format.
initialize,AASequence-method "AASequence" Object representation of a protein Sequence

-- L --

levels,AAAlphabet-method Class "AAAlphabet" Amino Acid Alphabet
listdist Compute distance matrix from a list
listdist,list-method Compute distance matrix from a list
listdist-methods Compute distance matrix from a list

-- R --

readFasta reader for databases in Fasta file format.
readFasta,AASequence-method reader for databases in Fasta file format.
readFasta,AASequenceList-method reader for databases in Fasta file format.
readFasta-methods reader for databases in Fasta file format.

-- S --

salign Optimal pairwise alignment of two protein sequences.
salign,AASequence,AASequence-method Optimal pairwise alignment of two protein sequences.
salign,AASequence,AASequenceList-method Optimal pairwise alignment of two protein sequences.
salign,AASequenceList,AASequence-method Optimal pairwise alignment of two protein sequences.
salign,AASequenceList,NULL-method Optimal pairwise alignment of two protein sequences.
salign-methods Optimal pairwise alignment of two protein sequences.
selfalign "AASequence" Object representation of a protein Sequence
selfalign,AASequence,Submatrix-method "AASequence" Object representation of a protein Sequence
seqgrep reader for databases in Fasta file format.
sequlist AASequenceList with 66 entries.
show,AAAlignment-method "AAAlignment" result of pairwise sequence alignment.
show,AAAlphabet-method Class "AAAlphabet" Amino Acid Alphabet
show,AASequence-method "AASequence" Object representation of a protein Sequence
show,AASequenceList-method Class "AASequenceList" - Container
show,Submatrix-method Class "Submatrix" Substitution Matrix
subFromEmboss Class "Submatrix" Substitution Matrix
subFromEmboss,Submatrix,character-method Class "Submatrix" Substitution Matrix
Submatrix Class "Submatrix" Substitution Matrix
Submatrix-class Class "Submatrix" Substitution Matrix
summary,AAAlignment-method "AAAlignment" result of pairwise sequence alignment.

-- T --

testalign Scoring of optimal alingments.
testalign,AASequence,AASequence-method Scoring of optimal alingments.
testalign-methods Scoring of optimal alingments.

-- misc --

[,AASequenceList-method Class "AASequenceList" - Container
[<-,AASequenceList-method Class "AASequenceList" - Container
[[<-,AASequenceList-method Class "AASequenceList" - Container