Index F

[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]

FASTA 
    flat file database, indexing 
    open source tools and 
feature formats, EMBOSS 
feature tables
    DDBJ/EMBL/GenBank 
    extracting CDS/mRNA/translations from 
    SWISS-PROT 
    writing representation of to standard output 
features 
    locations 
    masking 
    qualifiers 
    tables of  [See feature tables]
field definitions
    DDBJ flat files 
    EMBL flat files 
    GenBank flat files 
    Pfam flat files 
    PROSITE flat files 
    SWISS-PROT flat files 
files
    ABI sequence trace 
    ASCII, removing carriage returns from 
    codon usage table 
    coordinate 
        writing protein-heterogen contact data files from 
    dinucleotides, counting number of 
    domains coordinate files, writing from protein coordinate files 
    EMBL CD-ROM format index
        building from BLAST database 
        building from FASTA flat file database 
        building from flat file database 
        building from GCG-format database 
    EMBL-like format, writing SCOP classification to 
    EMBOSS data, determining directories that can hold 
    enzymatic data of, plottng 
    FASTA
        sequence entries in 
        zzz  [See also FASTA][See also FASTA]
    flat  [See flat files]
    hexanucleotides, counting number of 
    inter-chain residue-residue contact data
        writing 
    intra-chain residue-residue contact data 
    mass spectrometry result 
    PDB, parsing 
    profile matrix, creating from nucleic acid sequences 
    protein coordinate
        writing domains coordinate files from 
        writing from PDB files 
    SCOP classification
        converting/writing to EMBL-like format files 
        removing low-resolution domains from 
        removing redundant domains from 
    SWISS-PROT:PDB-equivalence, converting to EMBL-like format 
    trinucleotides, counting number of 
    typing sequences into 
findkm program (EMBOSS) 
flat file databases, indexing 
flat files 
    DDBJ example 
    EMBL example 
    GenBank example 
    Pfam example 
    PROSITE example 
    SWISS-PROT example 
flatworm mitochondrial code 
formatdb program 
formatdb program (BLAST) 
freak program (EMBOSS) 
frequency tables, codon 
funky program (EMBOSS) 
fuzznuc program (EMBOSS) 
fuzzpro program (EMBOSS) 
fuzztran program (EMBOSS) 



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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