# seqinr v1.0-1

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by seqinr

## seqinr

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data manadgment under the ACNUC system.

## Functions in seqinr

 Name Description plot.SeqAcnucWeb To Plot Subsequences on the Parent Sequence getAnnot Generic Function to obtain annotation for a sequence a Converts amino-acid three-letter code into the one-letter one EXP Vectors of coefficients to compute linear forms. c2s conversion of a vector of chars into a string invers invers lseqinr To see what's inside the package seqinr SeqFastadna Class for DNA sequence in Fasta Format get.db.growth Get the exponential growth of nucleic acid database content SeqAcnucWeb Sequence coming from an ACNUC data bases located on the web kaks to Get an Estimation of Ka and Ks computePI To Compute the Theoretical Isoelectric Point GC2 Calculates the fractional GC2 content of nucleic acid sequences s2n simple numerical encoding of a DNA sequence. SeqFrag Class for sub-sequences AAstat To Get Some Protein Statistics dia.bactgensize Distribution of bacterial genome size from GOLD count Composition of dimer/trimer/etc nucleotides GC3 Calculates the fractional GC3 content of nucleic acid sequences SeqFastaAA AA sequence in Fasta Format tablecode to plot genetic code as in textbooks n2s function to convert the numeric encoding of a DNA sequence into a vector of characters choosebank To select a database structured under ACNUC and located on the web oriloc Prediction of origin and terminus of replication in bacteria ec999 999 coding sequences from E. coli read.fasta Read file in fasta format gb2fasta conversion of GenBank file into fasta file getTrans Generic Function to translate a sequence getLength Generic Function To obtain the length of a sequence aaa Converts amino-acid one-letter code into the three-letter one getType To Get Sequence Type uco Create codon usage table words.pos Positions of possibly degenerated motifs within sequences dist.alignment Pairwise Distances from Aligned Protein or DNA/RNA Sequences getSequence Generic Function To Get a sequence translate Translate nucleic acid sequences getKeyword Generic Function to get keyword(s) associated to a sequence dotchart.uco Cleveland plot for codon usage tables words To get all words from an alphabet. chargaff Base composition in ssDNA for 7 bacterial DNA getName Generic Function To obtain the name of a sequence splitseq split a sequence into sub-sequences SEQINR.UTIL utility data for seqinr comp complement a nucleic sequence read.alignment Read file in mase, clustal, phylip, fasta or msf format gbk2g2 Conversion of a GenBank format file into a glimmer-like one s2c conversion of a string into a vector of chars get.ncbi Bacterial complete genome data from ncbi ftp site GC Calculates the fractional GC content of nucleic acid sequences getFrag Generic Function to obtain a fragment of a sequence getLocation Generic Function To obtain the Position of a Sequence on the Parent Sequence query To get a list of sequence names from an ACNUC data base located on the web closebank To close a remote ACNUC database dinucl Mean zscore on 242 complete bacterial chromosomes aacost Aerobic cost of amino-acids in Escherichia coli and G+C classes dotPlot Dot Plot Comparison of two sequences AnoukResult Expected numeric results for Ka and Ks computation prochlo Zscore on three strains of Prochlorococcus marinus synsequence Random synonymous coding sequence generation GetFromSequence Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence dinucleotides Statistical over- and under- representation of dinucleotides in a sequence permutation Sequence permutation according to several different models ucoweight Weight of each synonymous codon G+C Content Calculates the fractional G+C content of nucleic acid sequences pmw Protein Molecular Weight reverse.align Reverse alignment - from protein sequence alignment to nucleic sequence alignment toyaa A toy example of amino-acid counts in three proteins toycodon A toy example of codon counts in three coding sequences crelistfromclientdata To create on server a bitlist from data lines sent by client syncodons Synonymous codons write.fasta Write file in fasta format seqinr-package Biological Sequences Retrieval and Analysis aaindex List of 544 physicochemical and biological properties for the 20 amino-acids No Results!