Index P

[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)