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scorer |
Standard (Mandatory) qualifiers:
[-goldsequence] sequence Test aligned and substituted sequence
[-testsequence] sequence Gold standard aligned and substituted
sequence
[-outfile] outfile If you enter the name of a file here then
this program will write the score details
into that file.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-goldsequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-testsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-odirectory3 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-goldsequence] (Parameter 1) |
Test aligned and substituted sequence | Readable sequence | Required |
| [-testsequence] (Parameter 2) |
Gold standard aligned and substituted sequence | Readable sequence | Required |
| [-outfile] (Parameter 3) |
If you enter the name of a file here then this program will write the score details into that file. | Output file | <sequence>.scorer |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Under development, no example input file(s) yet
Under development, no example output file(s) yet
| Program name | Description |
|---|---|
| alignrunner | Align sequence pairs in a directory |
| comparator | Compare contact scores of two sequence alignments |
| contactalign | Damian Counsell's experimental 2.5-D alignment algorithm |
| esim4 | Align an mRNA to a genomic DNA sequence |
| est2genome | Align EST and genomic DNA sequences |
| nawalign | Damian Counsell's NW implementation |
| nawalignrunner | Nawalign all sequence pairs in a directory |
| needle | Needleman-Wunsch global alignment |
| needlerunner | Needle all sequence pairs in a directory |
| scorerrunner | SCORER for ordered pairs of substituted seqs |
| stretcher | Finds the best global alignment between two sequences |
| substitute | Substitute matches into a template |
| substituterunner | Run SUBSTITUTE on a directory of traces |