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contactalign |
Standard (Mandatory) qualifiers: [-querysequence] sequence First (query) polypeptide sequence to be aligned [-templatesequence] sequence Second (template) polypeptide sequence to be aligned -gapopen float The gap opening penalty is subtracted from the total score every time a gap is inserted in the alignment. The default value is chosen for the EBLOSUM62 scoring matrix when you are aligning protein sequences, and the EDNAFULL matrix when you are aligning nucleotide sequences. If you sequence contains many small errors you should set a low gap opening penalty (near zero) to avoid over-penalizing those errors. -gapextend float The gap extension penalty is the score substracted when more spaces are added to an existing alignment gap. Often a single insertion or deletion affects multiple residues/nucleotides; separate opening and extension penalties reduce the excessive penalty such events would otherwise carry; generally the gap extension penalty should be significantly lower than the gap opening penalty. [-alignedoutfile] seqout Output sequence USA Additional (Optional) qualifiers: -substitutionscoringfile matrixf Matrix of scores for specific amino acid residue type substitution within one-dimensional sequence strings -contactscoringfile matrixf Matrix of scores for frequency of contacts between specific amino acid residue types Advanced (Unprompted) qualifiers: -[no]zeroend boolean If this option is true then no penalty is added for gaps at either ends of a trace. Associated qualifiers: "-querysequence" 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 "-templatesequence" 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 "-alignedoutfile" associated qualifiers -osformat3 string Output seq format -osextension3 string File name extension -osname3 string Base file name -osdirectory3 string Output directory -osdbname3 string Database name to add -ossingle3 boolean Separate file for each entry -oufo3 string UFO features -offormat3 string Features format -ofname3 string Features file name -ofdirectory3 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 | |
---|---|---|---|
[-querysequence] (Parameter 1) |
First (query) polypeptide sequence to be aligned | Readable sequence | Required |
[-templatesequence] (Parameter 2) |
Second (template) polypeptide sequence to be aligned | Readable sequence | Required |
-gapopen | The gap opening penalty is subtracted from the total score every time a gap is inserted in the alignment. The default value is chosen for the EBLOSUM62 scoring matrix when you are aligning protein sequences, and the EDNAFULL matrix when you are aligning nucleotide sequences. If you sequence contains many small errors you should set a low gap opening penalty (near zero) to avoid over-penalizing those errors. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence |
-gapextend | The gap extension penalty is the score substracted when more spaces are added to an existing alignment gap. Often a single insertion or deletion affects multiple residues/nucleotides; separate opening and extension penalties reduce the excessive penalty such events would otherwise carry; generally the gap extension penalty should be significantly lower than the gap opening penalty. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence |
[-alignedoutfile] (Parameter 3) |
Output sequence USA | Writeable sequence | <sequence>.format |
Additional (Optional) qualifiers | Allowed values | Default | |
-substitutionscoringfile | Matrix of scores for specific amino acid residue type substitution within one-dimensional sequence strings | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
-contactscoringfile | Matrix of scores for frequency of contacts between specific amino acid residue types | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-[no]zeroend | If this option is true then no penalty is added for gaps at either ends of a trace. | Boolean value Yes/No | Yes |
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 |
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 |
substitute | Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence) |
substituterunner | Runs substitute on directory of traces and writes substituted sequences to another |