A C D E G I K L N O P Q R S T U W Z
seqinr-package | Biological Sequences Retrieval and Analysis |
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 |
AAstat | To Get Some Protein Statistics |
AnoukResult | Expected numeric results for Ka and Ks computation |
as.SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web |
as.SeqFastaAA | AA sequence in Fasta Format |
as.SeqFastadna | Class for DNA sequence in Fasta Format |
as.SeqFrag | Class for sub-sequences |
c2s | conversion of a vector of chars into a string |
chargaff | Base composition in ssDNA for 7 bacterial DNA |
choosebank | To select a database structured under ACNUC and located on the web |
closebank | To close a remote ACNUC database |
comp | complements a nucleic acid sequence |
computePI | To Compute the Theoretical Isoelectric Point |
count | Composition of dimer/trimer/etc nucleotides |
crelistfromclientdata | To create on server a bitlist from data lines sent by client |
dia.bactgensize | Distribution of bacterial genome size from GOLD |
dia.db.growth | Get the exponential growth of nucleic acid database content |
dinucl | Mean zscore on 242 complete bacterial chromosomes |
dist.alignment | Pairwise Distances from Aligned Protein or DNA/RNA Sequences |
dotchart.uco | Cleveland plot for codon usage tables |
dotPlot | Dot Plot Comparison of two sequences |
ec999 | 999 coding sequences from E. coli |
EXP | Vectors of coefficients to compute linear forms. |
gb2fasta | conversion of GenBank file into fasta file |
gbk2g2 | Conversion of a GenBank format file into a glimmer-like one |
GC | Calculates the fractional G+C content of nucleic acid sequences |
GC1 | Calculates the fractional G+C content of nucleic acid sequences |
GC2 | Calculates the fractional G+C content of nucleic acid sequences |
GC3 | Calculates the fractional G+C content of nucleic acid sequences |
get.db.growth | Get the exponential growth of nucleic acid database content |
get.ncbi | Bacterial complete genome data from ncbi ftp site |
getAnnot | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getAnnots | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getAttributsocket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getExon | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getFrag | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getKeyword | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getKeywordsocket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getLength | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getLocation | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getLocationSocket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getName | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getNumber.socket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getSequence | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getSequenceSocket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getTrans | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
getType | To Get Sequence Type |
invers | invers |
is.SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web |
is.SeqFastaAA | AA sequence in Fasta Format |
is.SeqFastadna | Class for DNA sequence in Fasta Format |
is.SeqFrag | Class for sub-sequences |
kaks | to Get an Estimation of Ka and Ks |
lseqinr | To see what's inside the package seqinr |
n2s | function to convert the numeric encoding of a DNA sequence into a vector of characters |
ncbi.fna.url | Bacterial complete genome data from ncbi ftp site |
ncbi.gbk.url | Bacterial complete genome data from ncbi ftp site |
ncbi.ptt.url | Bacterial complete genome data from ncbi ftp site |
ncbi.stats | Bacterial complete genome data from ncbi ftp site |
oriloc | Prediction of origin and terminus of replication in bacteria |
parser.socket | Sequence coming from an ACNUC data bases located on the web |
permutation | Sequence permutation according to several different models |
plot.SeqAcnucWeb | To Plot Subsequences on the Parent Sequence |
pmw | Protein Molecular Weight |
print.qaw | To get a list of sequence names from an ACNUC data base located on the web |
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.alignment | Read aligned sequence files in mase, clustal, phylip, fasta or msf format |
read.fasta | read FASTA formatted files |
readAnnots.socket | Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence |
removeTrailingSpaces | To select a database structured under ACNUC and located on the web |
reverse.align | Reverse alignment - from protein sequence alignment to nucleic sequence alignment |
rho | Statistical over- and under- representation of dinucleotides in a sequence |
s2c | conversion of a string into a vector of chars |
s2n | simple numerical encoding of a DNA sequence. |
SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web |
SeqFastaAA | AA sequence in Fasta Format |
SeqFastadna | Class for DNA sequence in Fasta Format |
SeqFrag | Class for sub-sequences |
seqinr | Biological Sequences Retrieval and Analysis |
SEQINR.UTIL | utility data for seqinr |
simon | To get a list of sequence names from an ACNUC data base located on the web |
splitseq | split a sequence into sub-sequences |
summary.SeqFastaAA | AA sequence in Fasta Format |
summary.SeqFastadna | Class for DNA sequence in Fasta Format |
syncodons | Synonymous codons |
synsequence | Random synonymous coding sequence generation |
tablecode | to plot genetic code as in textbooks |
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 |
uco | Codon usage indices |
ucoweight | Weight of each synonymous codon |
words | To get all words from an alphabet. |
words.pos | Positions of possibly degenerated motifs within sequences |
write.fasta | Write file in fasta format |
zscore | Statistical over- and under- representation of dinucleotides in a sequence |