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comparator |
Standard (Mandatory) qualifiers: [-goldpairseqset] seqset pair of gold standard aligned aa sequences to be substituted [-testpairseqset] seqset pair of aligned aa sequences to be substituted [-contactscoringfile] matrixf Matrix of scores for frequency of contacts between specific amino acid residue types [-cmaptemplate] infile contact map of template structure [-scoringtrace] outfile scored vertical trace of template sequence against both alignments Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-goldpairseqset" 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 "-testpairseqset" associated qualifiers -sbegin2 integer Start of each sequence to be used -send2 integer End of each 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 "-scoringtrace" associated qualifiers -odirectory5 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 | |
---|---|---|---|
[-goldpairseqset] (Parameter 1) |
pair of gold standard aligned aa sequences to be substituted | Readable set of sequences | contacttest/1hgxa0_1hmpa0.ali |
[-testpairseqset] (Parameter 2) |
pair of aligned aa sequences to be substituted | Readable set of sequences | contacttest/1hgx_a_1hmp_a.fasta |
[-contactscoringfile] (Parameter 3) |
Matrix of scores for frequency of contacts between specific amino acid residue types | Comparison matrix file in EMBOSS data path | contactscores.dat |
[-cmaptemplate] (Parameter 4) |
contact map of template structure | Input file | 1hgx_a.con |
[-scoringtrace] (Parameter 5) |
scored vertical trace of template sequence against both alignments | Output file | scored.trace |
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 |
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 |
substitute | Substitute matches into a template |
substituterunner | Run SUBSTITUTE on a directory of traces |