[SYMBOL]
[A]
[B]
[C]
[D]
[E]
[F]
[G]
[H]
[I]
[J]
[K]
[L]
[M]
[N]
[O]
[P]
[Q]
[R]
[S]
[T]
[U]
[V]
[W]
[Y]
pairwise sequence alignment formats, EMBOSS
palindrome program (EMBOSS)
parse dictionary of heterogen groups
pasteseq program (EMBOSS)
patmatdb program (EMBOSS)
patmatmotifs program (EMBOSS)
Pattern-Hit Initiated BLAST (PHI-BLASTÑsee PHI-BLAST program)
patterns
PCR reactions, selecting primers for
PDB files, parsing
pdbpars program (EMBOSS)
pdbtosp program (EMBOSS)
pepcoil program (EMBOSS)
pepinfo program (EMBOSS)
pepnet program (EMBOSS)
pepstats program (EMBOSS)
peptide sequences
determining where proteolytic enzymes might cut
displaying in helical representation
pepwheel program (EMBOSS)
pepwindow program (EMBOSS)
pepwindowall program (EMBOSS)
Pfam
flat files
example
field definitions
PHI-BLAST (Pattern-Hit Initiated BLASTÑsee PHI-BLAST program)
PHI-BLAST program (BLAST)
PROSITE conventions
phylogenetic analysis
plant plastid code
plotcon program (EMBOSS)
plotorf program (EMBOSS)
polydot program (EMBOSS)
Position-Specific Iterated BLAST (PSI-BLASTÑsee PSI-BLAST program)
preg program (EMBOSS)
pressdb program
prettyplot program (EMBOSS)
prettyseq program (EMBOSS)
primer pairs, searching against sequences
primer3 program, eprimer3 program as interface to
primersearch program (EMBOSS)
PRINTS databases
preprocessing for use with PSCAN program
printsextract program (EMBOSS)
profgen program (EMBOSS)
profile matrix files, creating from nucleic acid sequences
profiles
profit program (EMBOSS)
programs
BLAST
EMBOSS
table of
HMMER
prophecy program (EMBOSS)
prophet program (EMBOSS)
prosextract program (EMBOSS)
PROSITE
flat files
example
field definitions
PHI-BLAST program and
PROSITE motif databases
protein coordinate files
writing domains coordinate files from
writing from PDB files
protein databases, matching mass spectrometry data in
protein functions, determining
protein motifs
comparing to PROSITE motif database
comparing to protein sequences
finding helix-turn-helix nucleic acid binding in
identifying quickly
protein sequences
antigenic regions
calculating multiple alginment of
charges to amino acids
creating profile matrix file from
determining nucleic acid sequence source
displaying
publication format
displaying graph of Kyte & Doolittle hydropathy plot of
displaying in publication format
metrics about
producing cDNA sequences from
reports about
searching for match of regular expression to
searching with PROSITE-style patterns
stops in
protein signal cleavage sites, reporting
protein-heterogen contact data files, writing from coordinate files
proteins
calculating isoelectric point of
displaying residues of
newly discovered
predicting transmembrane segments in
protein coding regions, analyzing
protein hydropathy, displaying
scanning with PRINTS
proteolytic enzymes
protozoan code
PSCAN program
pscan program (EMBOSS)
PSI-BLAST (Position-Specific Iterated BLASTÑsee PSI-BLAST program)
PSI-BLAST program (BLAST)
psiblast program (EMBOSS)
|