Index S

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sample sequence formats, FASTA entry 
scenedesmus obliquus mitochondrial code 
SCOP classification files 
scopalign program (EMBOSS) 
scope program (EMBOSS) 
scopnr program (EMBOSS) 
scopparse program (EMBOSS) 
scoprep program (EMBOSS) 
scopreso program (EMBOSS) 
scopseqs program (EMBOSS) 
secondary structures
    predicting  2nd 
    SWISS-PROT feature table 
seealso program (EMBOSS) 
seed alignments 
seqalign program (EMBOSS) 
seqmatchall program (EMBOSS) 
seqret program (EMBOSS) 
seqretsplit program (EMBOSS) 
seqsearch program (EMBOSS) 
seqsort program (EMBOSS) 
sequence analysis
    subfields of 
    tools for performing, list of 
sequence annotation 
sequence data lines, FASTA 
sequence databases 
    MAST and 
    table listing ways to access 
sequence formats
    EMBOSS 
        input 
        output 
    FASTA  [See FASTA]
sequences
    aligned 
        alignment formats 
        plotting quality of conservation of 
        removing gaps from 
        using Smith-Waterman algorithm 
    cDNA, producing from aligned protein sequences 
    comparing  2nd 
        all-against-all pairwise 
        matching words of specified length 
        nonoverlapping wordmatch plot display 
    comparing/matching with BLAST 
    concatenating 
    CpG areas in 
    creating game representation plots for 
    descriptive text of, searching 
    displaying 
    DNA
        predicting cut sites in 
        predicting twisting of 
    editing  2nd 
    EST, trimming poly-A tails off 
    excluding 
    extracting 
        pairs of 
    finding matches with GRIBSKOV/HENIKOFF profiles 
    finding optimum alignment of 
    identifying CpG regions in 
    inserting one into another 
    listing information about  2nd 
    listing properties of 
    masking features of 
    matching 
    merging 
    multiple alignment
        calculating consensus sequence from 
        calculating evolutionary distances between 
    mutating 
    names of, adding to list file 
    nucleic acid
        calculating fraction of G+C bases of 
        calculating melting temperature of 
        calculating multiple alignment of 
        calculating percent G+C of 
        creating profile matrix file from 
        displaying in publication format  2nd 
        displaying protein translation in publication format 
        finding MAR/SAR sites in 
        finding recognition sites in 
        matching to regular expressions 
        merging 
        scanning for silent mutation restriction enzyme sites 
        searching with PROSITE-style protein patterns 
        translating to peptide sequences 
    nucleotide
        inverted repeats in  2nd 
        scanning for dinucleotide CG 
        scanning for restriction sites 
        searching with PROSITE-style patterns 
    of ORFs 
    outputting reverse complement of 
    peptide
        determining where proteolytic enzymes might cut 
        displaying in helical representation 
        translating to nucleic acid sequences 
    plotting GC content over 
    protein  [See also protein sequences][See also protein sequences]
        searching for match of regular expression to 
    randomly shuffling order of 
    reading/writing 
        in individual files 
    regions of 
        masking off 
        removing 
    reporting differences between 
    retrieving from SWISS-PROT 
    scanning for tandem repeats 
    searching EMBOSS databases for 
    searching for bases/residues 
    searching primer pairs against 
    set of, comparing 
    skipping 
    spliced nucleotide, aligning to unspliced genomic DNA sequences 
    stripping vector sequences from 
    tandem repeats in 
    tidying up ends of 
    TRANSFAC, matching against input sequences 
    typing into files 
seqwords program (EMBOSS) 
setdb program 
showalign program (EMBOSS) 
showdb program (EMBOSS) 
showfeat program (EMBOSS) 
showorf program (EMBOSS) 
showseq program (EMBOSS) 
shuffleseq program (EMBOSS) 
SIB (Swiss Institute of Bioinformatics) 
side chains of amino acids 
sigcleave program (EMBOSS) 
siggen program (EMBOSS) 
sigscan program (EMBOSS) 
silent mutation restriction enzyme sites, scanning nucleic acid sequences for 
silent program (EMBOSS) 
skipseq program (EMBOSS) 
Smith-Waterman algorithm, calculating local alignment 
spiroplasma code 
spliced nucleotide sequences, aligning to unspliced genomic DNA sequences 
standard code 
stretcher program (EMBOSS) 
stssearch program (EMBOSS) 
supermatcher program (EMBOSS) 
Swiss Institute of Bioinformatics (SIB) 
SWISS-PROT 
    feature table  [See SWISS-PROT feature table]
    flat files
        example 
        field definitions 
    retrieving sequences from 
SWISS-PROT feature table 
    amino-acid modifications 
        lipid moiety attached groups 
        most frequently used 
    change indicators 
    regions 
    secondary structure 
SWISS-PROT:PDB-equivalence files, converting to EMBL-like format 
swissparse program (EMBOSS) 
syco program (EMBOSS)