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Abstract Syntax Notation One  [See ASN.1]
Accelrys package 
accession number
    blastn and 
    FASTA files and 
    fastacmd parameter  2nd 
    formatdb parameter 
    megablast parameter 
    NCBI identifier 
    one-to-one mapping 
    public databases and  2nd 
    sequence records and  2nd  3rd 
    xdformat parameter 
    xdget parameter 
actual length  2nd 
adenine (A)  2nd 
affine gaps
    blastall parameter 
    defined 
    megablast parameter  2nd  3rd 
AG-BLAST  2nd 
alanine (A) 
algorithms  [See also two-hit algorithm][See also two-hit algorithm]
    alignment  2nd  3rd 
    big-O notation 
    BLAST 
    BLAT 
    HMMER 
alias databases
    features 
    formatdb and  2nd  3rd  4th 
    GI numbers and 
    WU/NCBI-BLAST differences 
alignment
    algorithms  2nd  3rd 
    alternate views 
    BLAST reporting  2nd 
    blastall parameter 
    blastpgp parameter 
    cross-species exploration 
    defined 
    determining significance 
    ESTs and 
    gaps and 
    insensitive search 
    mapping and 
    number expected by chance 
    overcalling and 
    percent identity and 
    query chopping and 
    repeats and 
    score metric 
    search space and 
    stop codons  2nd  3rd 
    sum score 
    TBLASTN 
    TBLASTX 
    vectors 
alignment groups
    BLAST report  2nd 
    exons and 
    links and topcomboN 
    WU-BLAST 
alignment threshold  2nd 
Alignments option (report) 
allele frequencies 
alleles  2nd 
Altivec 
Altschul, Stephen 
altscore parameter (WU-BLAST)  2nd 
amino acid similarity  2nd 
amino acids (aa)
    databases 
    difficulty sequencing 
    genetic code 
    PHI-BLAST and 
    proteins and  2nd 
    PSI-BLAST and 
    scoring matrices 
    symbols listed 
annealing 
annotating
    concatenating lines and 
    ESTs  2nd 
Apple Computer 
Archaea 
arginine (R)  2nd  3rd 
ASCII format 
ASN.1 (Abstract Syntax Notation One)
    bl2seq parameter 
    format  2nd 
    formatdb parameter 
    reports and 
asparagine (N)  2nd 
aspartate (D)  2nd 
asterisk (*)  2nd 
ATG (start codon) 

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