2.391 Restriction Enzyme analysis Mangalam nucleic:restriction tacg tacg perl "tacg" 0 sequence DNA Sequence (raw sequence) perl " < $value " 100 13 input_options Input options 2 beginning Beginning of a subsequence in your sequence (-b) perl ($value)? " -b $value" : "" end End of a subsequence in your sequence (-e) perl ($value)? " -e $value" : "" topology Form (or topology) of DNA (-f) perl (defined $value && $value != $vdef)? " -f $value" : "" 1 0 0: circular 1 1: linear degeneracy Degeneracy flag - controls input and analysis of degenerate sequence input (-D) perl ($value && $value != $vdef)? " -D $value" : "" 1 0 0: FORCES excl'n of degens in seq; only 'acgtu' accepted 1 1: cut as NONdegen unless degen's found; then cut as '-D3' 2 2: degen's OK; ignore in KEY, but match outside of KEY 3 3: degen's OK; expand in KEY, find only EXACT matches 4 4: degen's OK; expand in KEY, find ALL POSSIBLE matches codon Codon Usage table to use for translation (-C) perl ($value)? " -C $value" : "" 0 0 0: Universal 1 1: Mito_Vertebrates 2 2: Mito_Drosophila 3 3: Mito_S_Cervisiae 4 4: Mito_S_Pombe 5 5: Mito_N_crassa 6 6: Mito_Higher_Plants 7 7: Ciliates output_options Output options 2 order_by_cut Order the output by number of cuts/fragments (-c) perl ($value)? " -c" : "" 0 2 perl $print_fragments || $sites || $ladder_map || $gel_map width Output width (between 60 and 210) (-w) perl ($value && $value ne $vdef)? " -w $value" : "" 60 2 graphic Histogram output (-G) perl ($value)? " -G$binsize,$value" : "" 2 X X: horizontal X axis Y Y: vertical X axis Z Z: long output binsize Step size in histogram perl "" 2 perl $graphic selection_options Enzymes Selection options 2 enzymes Enzymes selection list (separated by comma) perl ($value)? " -r $value" : "" 2 max_cut Maximum number of cuts allowed in sequence (-M) perl ($value)? " -M $value" : "" 2 min_cut Minimum number of cuts in sequence for the enzyme to be selected (-m) perl ($value)? " -m $value" : "" 2 magnitude Select enzymes by magnitude of recognition site (-n) perl ($value && $value ne $vdef)? " -n $value" : "" 3 2 3 3 4 4 5 5 6 6 7 7 8 8 The 'magnitude' of the recognition sequence depends on the number of defined bases that make up the site. Degenerate bases can also contribute: acgt each count '1' magnitude point yrwsmk each count '1/2' magnitude point bdhu each count '1/4' magnitude point n doesn't count at all Those enzymes sequences' patterns that 'sum' to the equivalent of at least the given magnitude pass the test Examples: tgca=4, tgyrca=5, tgcnnngca=6, etc... The values are upwardly inclusive (5=5,6,7,8 6=6,7,8 ...) overhang Select enzymes by overhang generated (-o) perl (defined $value && $value ne $vdef)? " -o $value" : "" 1 2 5 5: 5' overhang 3 3: 3' 0 0: blunt (no overhang) 1 1: all analyses Analyses 2 summary Summary of site information (-s) perl ($value)? " -s" : "" 1 2 print_fragments Table of fragments (-F) perl ($value)? " -F $value" : "" 0 2 0 0: don't print fragments 1 1: by sites 2 2: sorted by sizes 3 3: both sites Table of actual cut sites (a la Strider) (-S) perl ($value)? " -S" : "" 0 2 ladder_map Ladder map of selected enzymes (-l) perl ($value)? " -l" : "" 2 gel_map Pseudo-graphic gel map (-g) perl ($value)? " -g $cutoff" : "" 2 cutoff Low-end cutoff in number of bases for gel map (>= 10) perl "" 2 You can cut off any size in 10^n increments (as you might want to cut off very large fragments if you were doing chromosomal digests). perl $gel_map linear_map_options Linear map 2 linear_map Linear map a la Strider (-L) perl ($value)? " -L" : "" 2 translation Linear co-translation (-t,-T) perl ($value)? " $trans_flag $translation_frames" : "" 2 no message 1 perl $three_letter && ($trans_flag="-T") && 0 no message 2 perl ! $three_letter && ($trans_flag="-t") && 0 perl $linear_map translation_frames Translation in how many frames 1 2 1 1 frame 3 3 frames 6 6 frames perl $translation three_letter Translation in 3-letter code (-T) perl "" 0 2 perl $translation orf_options Open Reading Frames 2 orf Do an ORF analysis perl ($value)? " -O $frame,$min_size" : "" 2 no message perl ($frame=~ s/\\s//g) && 0 frame Frames to search perl "" 1 2 1 1 2 2 3 3 4 4 5 5 6 6 perl $orf '" "' min_size Min ORF size perl "" 2 perl $orf pattern_search_options Pattern Search 2 pattern_search Do a pattern search (-p) perl ($value)? " -p $name,$pattern,$errors" : "" 2 pattern Pattern (<30 IUPAC character) perl "" 2 perl $pattern_search errors Max number of errors that are tolerated (<6) (-p) perl "" 0 2 perl $pattern_search name Label of pattern perl "" pattern1 2 perl $pattern_search proximity_options Search for spatial relationships between factors (-P) 2 proximity Do a proximity search perl ($value)? " -P $nameA,$distance,$nameB" : "" distance Distance between factors perl "" Distance specification: [+-][lg]Dist_Lo[-Dist_Hi + NameA is DOWNSTREAM of NameB (default is either) - NameA is UPSTREAM of NameB (ditto) l NameA is LESS THAN Dist_Lo from NameB (default) g NameA is GREATER THAN Dist_Lo from NameB examples: HindIII,350,bamhi: Matches HindIII sites within 350 bp of BamHI sites Pit1,-30-2500,Tataa: Match Pit1 sites 30 to 2500 bp UPSTREAM of a Tataa site perl $proximity nameA Name of first factor (nameA) perl "" NameA and NameB must be enzymes names (Rebase db) perl $proximity nameB Name of second factor (nameB) perl "" perl $proximity quiet perl " -q" 1