|
|
substitute |
Standard (Mandatory) qualifiers:
[-alignedpairsequence] seqset Pair of polypeptide sequences to be
substituted
[-substitutedoutseq] seqout Output sequence USA
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-alignedpairsequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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
"-substitutedoutseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 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 | |
|---|---|---|---|
| [-alignedpairsequence] (Parameter 1) |
Pair of polypeptide sequences to be substituted | Readable set of sequences | Required |
| [-substitutedoutseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
| 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 |
| scorer | Score alignments using structural alignments |
| scorerrunner | SCORER for ordered pairs of substituted seqs |
| stretcher | Finds the best global alignment between two sequences |
| substituterunner | Run SUBSTITUTE on a directory of traces |