/usr/lib/R/site-library/seqinr/INDEX is in r-cran-seqinr 3.3-3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 | AAstat To Get Some Protein Statistics
AnoukResult Expected numeric results for Ka and Ks
computation
ECH Forensic Genetic Profile Allelic Ladder Raw
Data
EXP Vectors of coefficients to compute linear
forms.
GC Calculates the fractional G+C content of
nucleic acid sequences.
JLO Forensic Genetic Profile Raw Data
SEQINR.UTIL utility data for seqinr
SeqAcnucWeb Sequence coming from a remote ACNUC data base
SeqFastaAA AA sequence in Fasta Format
SeqFastadna Class for DNA sequence in Fasta Format
SeqFrag Class for sub-sequences
a Converts amino-acid three-letter code into the
one-letter one
aaa Converts amino-acid one-letter code into the
three-letter one
aacost Aerobic cost of amino-acids in Escherichia coli
and G+C classes
aaindex List of 544 physicochemical and biological
properties for the 20 amino-acids
acnucopen open and close a remote access to an ACNUC
database
al2bp To Convert a forensic microsatellite allele
name into its length in base pairs
alllistranks To get the count of existing lists and all
their ranks on server
amb Expansion of IUPAC nucleotide symbols
as.alignment Constructor for class alignment
as.matrix.alignment as.matrix.alignment
autosocket Returns a socket to the last opened database
baselineabif Estimation of baseline value
bma Computing an IUPAC nucleotide symbol
c2s conversion of a vector of chars into a string
cai Codon Adaptation Index
caitab Codon Adaptation Index (CAI) w tables
chargaff Base composition in ssDNA for 7 bacterial DNA
choosebank To select a database structured under ACNUC and
located on the web
circle Draws a circle
closebank To close a remote ACNUC database
clustal Example of results obtained after a call to
read.alignment
col2alpha To use a standard color with an alpha
transparency chanel
comp complements a nucleic acid sequence
computePI To Compute the Theoretical Isoelectric Point
consensus Consensus and profiles for sequence alignments
count Composition of dimer/trimer/etc oligomers
countfreelists The number of free lists available and
annotation lines in an ACNUC server
countsubseqs Number of subsequences in an ACNUC list
crelistfromclientdata To create on server an ACNUC list from data
lines sent by client
dia.bactgensize Distribution of bacterial genome size from GOLD
dinucl Mean zscore on 242 complete bacterial
chromosomes
dist.alignment Pairwise Distances from Aligned Protein or
DNA/RNA Sequences
dotPlot Dot Plot Comparison of two sequences
dotchart.uco Cleveland plot for codon usage tables
draw.oriloc Graphical representation for nucleotide skews
in prokaryotic chromosomes.
draw.rearranged.oriloc
Graphical representation for rearranged
nucleotide skews in prokaryotic chromosomes.
draw.recstat Graphical representation of a recstat analysis.
ec999 999 coding sequences from E. coli
extract.breakpoints Extraction of breakpoint positions on the
rearranged nucleotide skews.
extractseqs To extract the sequences information of a
sequence or a list of sequence in different
formats
fasta Example of results obtained after a call to
read.alignment
fastacc Fast Allele in Common Count
gb2fasta Conversion of GenBank file into fasta file
gbk2g2 Conversion of a GenBank format file into a
glimmer-like one
gbk2g2.euk Conversion of a GenBank format file into a
glimmer-like one. Eukaryotic version.
gcO2 GC content and aerobiosis in bacteria
gcT GC content and temperature in bacteria
get.db.growth Get the exponential growth of nucleic acid
database content
get.ncbi Bacterial complete genome data from ncbi ftp
site
getAnnot Generic Function to get sequence annotations
getFrag Generic function to extract sequence fragments
getKeyword Generic function to get keywords associated to
sequences
getLength Generic function to get the length of sequences
getLocation Generic function to get the location of
subsequences on the parent sequence
getName Generic function to get the names of sequences
getSequence Generic function to get sequence data
getTrans Generic function to translate coding sequences
into proteins
getType To get available subsequence types in an opened
ACNUC database
getlistrank To get the rank of a list from its name
getliststate Asks for information about an ACNUC list of
specified rank
gfrag Extract sequence identified by name or by
number from an ACNUC server
ghelp Get help from an ACNUC server
gs500liz GS500LIZ size standards
identifiler Identifiler allele names
isenum Get the ACNUC number of a sequence from its
name or accession number
kaks Ka and Ks, also known as dn and ds, computation
knowndbs Description of databases known by an ACNUC
server
lseqinr To see what's inside the package seqinr
m16j Fragment of the E. coli chromosome
mase Example of results obtained after a call to
read.alignment
modifylist Modification of an ACNUC list
move Rename an R object
msf Example of results obtained after a call to
read.alignment
n2s function to convert the numeric encoding of a
DNA sequence into a vector of characters
oriloc Prediction of origin and terminus of
replication in bacteria.
pK pK values for the side chain of charged amino
acids from various sources
parser.socket Utility function to parse answers from an ACNUC
server
peakabif Extraction of Peak locations, Heights and
Surfaces from ABIF data
permutation Sequence permutation according to several
different models
phylip Example of results obtained after a call to
read.alignment
plot.SeqAcnucWeb To Plot Subsequences on the Parent Sequence
plotPanels Representation of Amplicon Size Ranges of a STR
kit.
plotabif Electrophoregram plot for ABIF data
plotladder Simple plot of an allelic ladder from ABIF data
pmw Protein Molecular Weight
prepgetannots Select annotation lines in an ACNUC database
prettyseq Text representation of a sequence from an ACNUC
server
print.SeqAcnucWeb Print method for objects from class SeqAcnucWeb
print.qaw Print method for objects from class qaw
prochlo Zscore on three strains of Prochlorococcus
marinus
query To get a list of sequence names from an ACNUC
data base located on the web
read.abif Read ABIF formatted files
read.alignment Read aligned sequence files in mase, clustal,
phylip, fasta or msf format
read.fasta read FASTA formatted files
readBins Import GenMapper Bins configuration file
readPanels Import GenMapper Panels configuration file
readfirstrec Low level function to get the record count of
the specified ACNUC index file
readsmj Low level function to read ACNUC SMJYT index
files
rearranged.oriloc Detection of replication-associated effects on
base composition asymmetry in prokaryotic
chromosomes.
recstat Prediction of Coding DNA Sequences.
residuecount Total number of residues in an ACNUC list
revaligntest Three aligned nucleic acid sequences
reverse.align Reverse alignment - from protein sequence
alignment to nucleic sequence alignment
rho Statistical over- and under- representation of
dinucleotides in a sequence
rot13 Ergheaf gur EBG-13 pvcurevat bs n fgevat
s2c conversion of a string into a vector of chars
s2n simple numerical encoding of a DNA sequence.
savelist Save sequence names or accession numbers into a
file
seqinr-package Biological Sequences Retrieval and Analysis
setlistname Sets the name of an ACNUC list identified by
its rank
splitseq split a sequence into sub-sequences
stresc Utility function to escape LaTeX special
characters present in a string
stutterabif Stutter ratio estimation
swap Exchange two R objects
syncodons Synonymous codons
synsequence Random synonymous coding sequence generation
tablecode to plot genetic code as in textbooks
test.co.recstat Tests if regions located between Stop codons
contain putative CDSs.
test.li.recstat Tests if regions located between Stop codons
contain putative CDSs.
toyaa A toy example of amino-acid counts in three
proteins
toycodon A toy example of codon counts in three coding
sequences
translate Translate nucleic acid sequences into proteins
trimSpace Trim leading and/or trailing spaces in strings
uco Codon usage indices
ucoweight Weight of each synonymous codon
waterabs Light absorption by the water column
where.is.this.acc Scans databases for a given sequence accession
number
words To get all words from an alphabet.
words.pos Positions of possibly degenerated motifs within
sequences
write.fasta Write sequence(s) into a file in fasta format
|