[SYMBOL]
[A]
[B]
[C]
[D]
[E]
[F]
[G]
[H]
[I]
[J]
[K]
[L]
[M]
[N]
[O]
[P]
[Q]
[R]
[S]
[T]
[U]
[V]
[W]
[X]
[Y]
[Z]
S= parameter (WU-BLAST)
Saccharomyces cereviseae
Saccharomyces Genome Database
same-sense mutations
saturated sequences
2nd
scaling factors
scientific experiments
controls and
designing
pilots and
searches as
scoring matrix
assumptions
bl2seq
blasta and
blastall
BLASTP
2nd
3rd
blastpgp
BLASTX
editing
2nd
expected score
footer reports
global alignment
2nd
insensitive search
local alignment
massaging statistics
overview
2nd
PSI-BLAST
relative entropy
RepeatMasker
report differences
target frequencies
troubleshooting
WU-BLAST
scoring schemes
BLAST parameters and
mapping oligo/genomes
massaging statistics
NCBI-BLAST
nucleotide
troubleshooting and
SCSI interface
search space
alignment
2nd
bl2seq parameter
blastall parameter
BLASTP
blastpgp parameter
cross-species sequence exploration
defined
depicted
HSP and
Karlin-Altschul statistics
2nd
3rd
mapping oligo/genomes
massaging statistics
searches
BLAST
BLASTP
2nd
choosing parameters
controls and
restricting
2nd
as scientific experiments
selecting database for
submitting
2° (secondary) structure
seeding
BLAST searches
BLASTN searches
BLASTX searches
cross-species exploration
insensitive search
2nd
mapping proteins/genomes
sensitivity and
short exons
soft masking and
troubleshooting
word size and
WU-BLAST and
2nd
seedp option (PHI-BLAST)
2nd
seedtop (NCBI-BLAST)
selfish DNA
sensitive searches
2nd
3rd
sensitivity
seeding and
specificity and
speed and
word size and
seqtest parameter (WU-BLAST)
sequence alignment
BLAST report
global alignment
local alignment
sequence databases
BLAST and
management strategies
sequence lines (FASTA format)
sequence management software
2nd
sequence similarity
amino acid similarity
BLAST and
2nd
cross-species exploration
determining
2nd
information theory
Karl-Altschul statistics
scoring matrices
2nd
sum statistics
target frequencies
sequences
classifying by
exploring and
FASTA format and
masking
molecular clocks and
search space between
transcripts for proteins
xdget
serial searches
accurate alignment
BLAST and
BLASTX and
long sequences
2nd
undocumented genes
serine (S)
2nd
setdb (WU-BLAST)
2nd
SGD database
SGE distributed resource management
Shannon's Entropy
Shannon, Claude
shotgun sequence
2nd
3rd
silent mutations
SIM4 program
similarity
biological sequences and
patterns of
vectors
weak
simple repeats
Smith-Waterman algorithm
[See also local alignment][See also local alignment]
alignment endpoints
BLAST statistics compared
blastpgp parameter
gold standard
soft masking
BLASTP searches
2nd
case sensitivity and
cross-species exploration
functionality
low-complexity and
seeding and
2nd
sensitive searches
software
optimization
sequence management
2nd
SOURCE (sequence record)
source code (NCBI-BLAST)
2nd
source, message and symbols from
sp2fasta (WU-BLAST file)
span parameter (WU-BLAST)
span1 parameter (WU-BLAST)
span2 parameter (WU-BLAST)
species
specificity
2nd
3rd
SPIDEY program
splicing
alternative
coding sequences and
regulation and
transcript clustering
SRS (Sequence Retrieval System)
stacking
start codons
statistics
[See also specific methods][See also specific methods]
massaging
2nd
redundant sequences and
statistical outliers
Stein, Lincoln
stop codon
alignment and
2nd
3rd
BLASTX
2nd
defined
mutation and
preventing
prokaryotic genes
pseudogenes
2nd
3rd
TBLASTX search
storage considerations
strandedness
BLAST
BLASTX
TBLASTX
sts database
Stuffit Expander
substitution matrix
[See scoring matrix]
substitution, nonconservative
sum score
alignments and
calculating
Expect and
2nd
overview
2nd
sumScore function
suppressors
SWISS-PROT database
2nd
symbolic links
symbols, message and
synonymous mutations
synteny
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