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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 | Runs alignment program on all sequence pairs in a directory |
contactalign | EMBOSS implementation of Damian Counsell's 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 implementation for protein sequences of the Needleman and Wunsch alignment algorithm |
nawalignrunner | Runs nawalign alignment program on all sequence pairs in a directory |
needle | Needleman-Wunsch global alignment |
needlerunner | Runs needle alignment program on all sequence pairs in a directory |
scorer | Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment |
scorerrunner | Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third |
stretcher | Finds the best global alignment between two sequences |
substituterunner | Runs substitute on directory of traces and writes substituted sequences to another |