[SYMBOL]
[A]
[B]
[C]
[D]
[E]
[F]
[G]
[H]
[I]
[J]
[K]
[L]
[M]
[N]
[O]
[P]
[Q]
[R]
[S]
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[Y]
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)
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