BIOBAR : USER MANUAL

Motif Discovery
o Gibbs Sampling
% GC of Genome – this value will be used to calculate the composition of
the genome sequence that the motif is scored upon
Window Length – this value determines the length of the window
sampled by Gibbs Sampling
Number of Iterations – the number of times the program should cycle
before reporting results (higher number of iterations means slower, but
more accurate results)
o Greedy Search
% GC of Genome – this value will be used to calculate the composition of
the genome sequence that the motif is scored upon
Window Length – this value determines the length of the window
sampled by Gibbs Sampling
Number of Iterations – the number of times the program should cycle
before reporting results (higher number of iterations means slower, but
more accurate results)
o Dyad Motif Search
Dyad Length – if values 5 ± 1 were entered, dyads of length 4, 5, and 6
will be considered
Spacer Length – if values 5 ± 1 were entered, spacers of length 4, 5, and 6
will be allowed
Mismatch Threshold – determines the maximum number of mismatches
that should be allowed between the two dyads
Palindrome – the dyads must be reverse complements of each other
Direct Repeat – the dyads must be identical
Pair-wise Alignment
o Scoring Options
The first selection allows the user to define constant values to be used to
score matches and mismatches
The second selection allows the user to define more specific values if
they would like to weigh certain mismatches/matches as less or more
important than another
NOTE: if protein sequences are selected, BLOSUM62 will be used to score
the matches and mismatches between the sequences
o GEP – this value defines the gap extension penalty
o GOP – this value defines the gap opening penalty
o Limit results to X alignments – in the case of split paths, the program will report
no more than X sequences