Biology Reference
In-Depth Information
process, at which time the trace-back matrix—an | s i |
| s j | matrix of
bytes, where | s k | is the length of sequence k—is necessary for the
backward portion of the dynamic programming procedure. If both
sequences being aligned are large relative to the computer's physi-
cal available memory, then this block of memory can become so
large that the computer spends a significant amount of processing
time paging physical memory to and from the system virtual
memory (i.e., hard-drive area). The value specified with this option
determines a maximum size of the trace-back matrix in bytes before
GRAMALIGN will (much more) efficiently copy pieces of the trace-
back matrix to “page files” within the current directory. At the end
of the trace-back procedure, these temporary page files will be
removed. Suggestion: For systems with larger physical memory,
this amount should be increased to improve performance. If this
option is not specified, the default value is 100 (i.e., 100 million
bytes). Note, the temporary page files are named _ga_temp.
page xxxxx , where xxxxx is replaced with the proper page number.
These files are safe to delete as long as GRAMALIGN is not running.
GRAMALIGN provides the following options for manipulating the
input and output files and their formats.
3.4
File Options
Option -i <filename>
: Specify the input file name, which needs to
be in FASTA format. If this option is not used, the default name
is “infile.” The type of input sequence (nucleotide or amino acid) is
determined by the input file type command-line option ( -F ).
Option -o <filename>
: Specify the output file name. If this option
is not used, the default file name is “outfile.”
Option -f <Value>
: Specify the output file format. A value of
0 will output the grammar-based distance matrix. A value of 1 will
output the alignment in PHYLIP format. A value of 2 will output
the alignment in Aligned FASTA format. A value of 3 will output
the alignment in MSF/GCG format. A value of 4 will output the
consensus sequence in html including gaps in the alignment.
A value of 5 will output the consensus sequence in html ignoring
any gap elements in the alignment. If this option is not specified,
the default file format is PHYLIP.
Option -F <Value>
: Specify the input file type. A value of 0 will
cause GRAMALIGN to automatically detect if the input file contains
amino acid sequences. The auto-detection is based on if a base
other than A, C, G, T, U, or X is part of the sequence. Should
any other character appear in any of the input sequences, the
program will align the sequences as though the input file contains
all amino acid sequences. A value of 1 will force the alignment to
assume all sequences are either DNA or RNA. A value of 2 will force
the alignment to assume all sequences are amino acid sequences.
If this option is not specified, the default is to automatically detect
the input file type.
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