# HG changeset patch # User iuc # Date 1529652269 14400 # Node ID 27c43fb015f0d38552886564eedd86d9ef842b7f # Parent d5c3794bd24611b499c8052b0f9996ce1b3baf18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753 diff -r d5c3794bd246 -r 27c43fb015f0 emboss_antigenic.xml --- a/emboss_antigenic.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_antigenic.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_backtranseq.xml --- a/emboss_backtranseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_backtranseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Back translate a protein sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_banana.xml --- a/emboss_banana.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_banana.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Bending and curvature plot in B-DNA macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_biosed.xml --- a/emboss_biosed.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_biosed.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Replace or delete sequence sections macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_btwisted.xml --- a/emboss_btwisted.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_btwisted.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Calculates the twisting in a B-DNA sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cai.xml --- a/emboss_cai.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cai.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + CAI codon adaptation index macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cai_custom.xml --- a/emboss_cai_custom.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cai_custom.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + CAI codon adaptation index using custom codon usage file macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_chaos.xml --- a/emboss_chaos.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_chaos.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Create a chaos game representation plot for a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_charge.xml --- a/emboss_charge.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_charge.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Protein charge plot macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_checktrans.xml --- a/emboss_checktrans.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_checktrans.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reports STOP codons and ORF statistics of a protein macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_chips.xml --- a/emboss_chips.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_chips.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Codon usage statistics macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cirdna.xml --- a/emboss_cirdna.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cirdna.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Draws circular maps of DNA constructs macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_codcmp.xml --- a/emboss_codcmp.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_codcmp.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Codon usage table comparison macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_coderet.xml --- a/emboss_coderet.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_coderet.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Extract CDS, mRNA and translations from feature tables macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_compseq.xml --- a/emboss_compseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_compseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Count composition of dimer/trimer/etc words in a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cpgplot.xml --- a/emboss_cpgplot.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cpgplot.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Plot CpG rich areas macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cpgreport.xml --- a/emboss_cpgreport.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cpgreport.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reports all CpG rich regions macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cusp.xml --- a/emboss_cusp.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cusp.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Create a codon usage table macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_cutseq.xml --- a/emboss_cutseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_cutseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Removes a specified section from a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_dan.xml --- a/emboss_dan.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_dan.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Calculates DNA RNA/DNA melting temperature macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_degapseq.xml --- a/emboss_degapseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_degapseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Removes gap characters from sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_descseq.xml --- a/emboss_descseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_descseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Alter the name or description of a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_diffseq.xml --- a/emboss_diffseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_diffseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Find differences between nearly identical sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_digest.xml --- a/emboss_digest.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_digest.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Protein proteolytic enzyme or reagent cleavage digest macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_dotmatcher.xml --- a/emboss_dotmatcher.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_dotmatcher.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays a thresholded dotplot of two sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_dotpath.xml --- a/emboss_dotpath.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_dotpath.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Non-overlapping wordmatch dotplot of two sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_dottup.xml --- a/emboss_dottup.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_dottup.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays a wordmatch dotplot of two sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_dreg.xml --- a/emboss_dreg.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_dreg.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Regular expression search of a nucleotide sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_einverted.xml --- a/emboss_einverted.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_einverted.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds DNA inverted repeats macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_epestfind.xml --- a/emboss_epestfind.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_epestfind.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds PEST motifs as potential proteolytic cleavage sites macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_equicktandem.xml --- a/emboss_equicktandem.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_equicktandem.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds tandem repeats macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_est2genome.xml --- a/emboss_est2genome.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_est2genome.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Align EST and genomic DNA sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_etandem.xml --- a/emboss_etandem.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_etandem.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Looks for tandem repeats in a nucleotide sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_extractfeat.xml --- a/emboss_extractfeat.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_extractfeat.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Extract features from a sequence diff -r d5c3794bd246 -r 27c43fb015f0 emboss_extractseq.xml --- a/emboss_extractseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_extractseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Extract regions from a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_freak.xml --- a/emboss_freak.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_freak.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Residue/base frequency table or plot macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_fuzzpro.xml --- a/emboss_fuzzpro.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_fuzzpro.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Protein pattern search macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_fuzztran.xml --- a/emboss_fuzztran.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_fuzztran.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Protein pattern search after translation macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_garnier.xml --- a/emboss_garnier.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_garnier.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Predicts protein secondary structure macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_geecee.xml --- a/emboss_geecee.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_geecee.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Calculates fractional GC content of nucleic acid sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_getorf.xml --- a/emboss_getorf.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_getorf.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds and extracts open reading frames (ORFs) macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_helixturnhelix.xml --- a/emboss_helixturnhelix.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_helixturnhelix.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Report nucleic acid binding motifs macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_hmoment.xml --- a/emboss_hmoment.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_hmoment.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Hydrophobic moment calculation macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_iep.xml --- a/emboss_iep.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_iep.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Calculates the isoelectric point of a protein macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_infoseq.xml --- a/emboss_infoseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_infoseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays some simple information about sequences diff -r d5c3794bd246 -r 27c43fb015f0 emboss_isochore.xml --- a/emboss_isochore.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_isochore.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Plots isochores in large DNA sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_lindna.xml --- a/emboss_lindna.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_lindna.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Draws linear maps of DNA constructs diff -r d5c3794bd246 -r 27c43fb015f0 emboss_marscan.xml --- a/emboss_marscan.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_marscan.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds MAR/SAR sites in nucleic sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_maskfeat.xml --- a/emboss_maskfeat.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_maskfeat.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Mask off features of a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_maskseq.xml --- a/emboss_maskseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_maskseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Mask off regions of a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_matcher.xml --- a/emboss_matcher.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_matcher.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds the best local alignments between two sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_megamerger.xml --- a/emboss_megamerger.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_megamerger.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Merge two large overlapping nucleic acid sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_merger.xml --- a/emboss_merger.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_merger.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Merge two overlapping nucleic acid sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_msbar.xml --- a/emboss_msbar.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_msbar.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Mutate sequence beyond all recognition macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_needle.xml --- a/emboss_needle.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_needle.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Needleman-Wunsch global alignment macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_newcpgreport.xml --- a/emboss_newcpgreport.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_newcpgreport.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Report CpG rich areas macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_newcpgseek.xml --- a/emboss_newcpgseek.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_newcpgseek.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reports CpG rich region macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_newseq.xml --- a/emboss_newseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_newseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Type in a short new sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_noreturn.xml --- a/emboss_noreturn.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_noreturn.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Removes carriage return from ASCII files macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_notseq.xml --- a/emboss_notseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_notseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Exclude a set of sequences and write out the remaining ones macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_nthseq.xml --- a/emboss_nthseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_nthseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Writes one sequence from a multiple set of sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_octanol.xml --- a/emboss_octanol.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_octanol.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays protein hydropathy diff -r d5c3794bd246 -r 27c43fb015f0 emboss_oddcomp.xml --- a/emboss_oddcomp.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_oddcomp.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Find protein sequence regions with a biased composition diff -r d5c3794bd246 -r 27c43fb015f0 emboss_palindrome.xml --- a/emboss_palindrome.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_palindrome.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Looks for inverted repeats in a nucleotide sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pasteseq.xml --- a/emboss_pasteseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pasteseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Insert one sequence into another macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_patmatdb.xml --- a/emboss_patmatdb.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_patmatdb.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Search a protein sequence with a motif macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepcoil.xml --- a/emboss_pepcoil.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepcoil.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Predicts coiled coil regions macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepinfo.xml --- a/emboss_pepinfo.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepinfo.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Plots simple amino acid properties in parallel diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepnet.xml --- a/emboss_pepnet.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepnet.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays proteins as a helical net diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepstats.xml --- a/emboss_pepstats.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepstats.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Protein statistics macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepwheel.xml --- a/emboss_pepwheel.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepwheel.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Shows protein sequences as helices diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepwindow.xml --- a/emboss_pepwindow.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepwindow.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays protein hydropathy diff -r d5c3794bd246 -r 27c43fb015f0 emboss_pepwindowall.xml --- a/emboss_pepwindowall.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_pepwindowall.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays protein hydropathy of a set of sequences diff -r d5c3794bd246 -r 27c43fb015f0 emboss_plotcon.xml --- a/emboss_plotcon.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_plotcon.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Plot quality of conservation of a sequence alignment diff -r d5c3794bd246 -r 27c43fb015f0 emboss_plotorf.xml --- a/emboss_plotorf.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_plotorf.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Plot potential open reading frames diff -r d5c3794bd246 -r 27c43fb015f0 emboss_polydot.xml --- a/emboss_polydot.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_polydot.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays all-against-all dotplots of a set of sequences diff -r d5c3794bd246 -r 27c43fb015f0 emboss_preg.xml --- a/emboss_preg.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_preg.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Regular expression search of a protein sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_prettyplot.xml --- a/emboss_prettyplot.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_prettyplot.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays aligned sequences, with colouring and boxing diff -r d5c3794bd246 -r 27c43fb015f0 emboss_prettyseq.xml --- a/emboss_prettyseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_prettyseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Output sequence with translated ranges macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_primersearch.xml --- a/emboss_primersearch.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_primersearch.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Searches DNA sequences for matches with primer pairs macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_revseq.xml --- a/emboss_revseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_revseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reverse and complement a sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_seqmatchall.xml --- a/emboss_seqmatchall.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_seqmatchall.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + All-against-all comparison of a set of sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_seqret.xml --- a/emboss_seqret.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_seqret.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reads and writes sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_showfeat.xml --- a/emboss_showfeat.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_showfeat.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Show features of a sequence diff -r d5c3794bd246 -r 27c43fb015f0 emboss_shuffleseq.xml --- a/emboss_shuffleseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_shuffleseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Shuffles a set of sequences maintaining composition diff -r d5c3794bd246 -r 27c43fb015f0 emboss_sigcleave.xml --- a/emboss_sigcleave.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_sigcleave.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reports protein signal cleavage sites macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_sirna.xml --- a/emboss_sirna.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_sirna.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds siRNA duplexes in mRNA macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_sixpack.xml --- a/emboss_sixpack.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_sixpack.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Display a DNA sequence with 6-frame translation and ORFs @@ -6,8 +6,12 @@ - sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase - '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto + @@ -47,7 +51,7 @@ - + @@ -104,7 +108,7 @@ - + .. class:: warningmark diff -r d5c3794bd246 -r 27c43fb015f0 emboss_skipseq.xml --- a/emboss_skipseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_skipseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reads and writes sequences, skipping first few macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_splitter.xml --- a/emboss_splitter.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_splitter.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Split a sequence into (overlapping) smaller sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_supermatcher.xml --- a/emboss_supermatcher.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_supermatcher.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Match large sequences against one or more other sequences diff -r d5c3794bd246 -r 27c43fb015f0 emboss_syco.xml --- a/emboss_syco.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_syco.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Synonymous codon usage Gribskov statistic plot diff -r d5c3794bd246 -r 27c43fb015f0 emboss_tcode.xml --- a/emboss_tcode.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_tcode.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Fickett TESTCODE statistic to identify protein-coding DNA macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_textsearch.xml --- a/emboss_textsearch.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_textsearch.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Search sequence documentation. Slow, use SRS and Entrez! macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_tmap.xml --- a/emboss_tmap.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_tmap.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Displays membrane spanning regions macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_tranalign.xml --- a/emboss_tranalign.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_tranalign.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Align nucleic coding regions given the aligned proteins macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_transeq.xml --- a/emboss_transeq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_transeq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Translate nucleic acid sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_trimest.xml --- a/emboss_trimest.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_trimest.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Trim poly-A tails off EST sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_trimseq.xml --- a/emboss_trimseq.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_trimseq.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Trim ambiguous bits off the ends of sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_twofeat.xml --- a/emboss_twofeat.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_twofeat.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds neighbouring pairs of features in sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_union.xml --- a/emboss_union.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_union.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Reads sequence fragments and builds one sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_vectorstrip.xml --- a/emboss_vectorstrip.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_vectorstrip.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Strips out DNA between a pair of vector sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_water.xml --- a/emboss_water.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_water.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Smith-Waterman local alignment macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_wobble.xml --- a/emboss_wobble.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_wobble.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Wobble base plot macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_wordcount.xml --- a/emboss_wordcount.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_wordcount.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Counts words of a specified size in a DNA sequence macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 emboss_wordmatch.xml --- a/emboss_wordmatch.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_wordmatch.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ - + Finds all exact matches of a given size between 2 sequences macros.xml diff -r d5c3794bd246 -r 27c43fb015f0 macros.xml --- a/macros.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/macros.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,7 +1,8 @@ + 5.0.0 - emboss + emboss diff -r d5c3794bd246 -r 27c43fb015f0 test-data/emboss_sixpack_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_sixpack_out.fasta Fri Jun 22 03:24:29 2018 -0400 @@ -0,0 +1,53 @@ +>Sequence_1_ORF1 Translation of Sequence in frame 1, ORF 1, threshold 1, 17aa +VRCLKYLLLSLHRPQFS +>Sequence_1_ORF2 Translation of Sequence in frame 1, ORF 2, threshold 1, 5aa +WLYTD +>Sequence_1_ORF3 Translation of Sequence in frame 1, ORF 3, threshold 1, 6aa +KFLCKH +>Sequence_1_ORF4 Translation of Sequence in frame 1, ORF 4, threshold 1, 12aa +LKAVGLECYRFV +>Sequence_1_ORF5 Translation of Sequence in frame 1, ORF 5, threshold 1, 33aa +LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC +>Sequence_1_ORF6 Translation of Sequence in frame 1, ORF 6, threshold 1, 25aa +LLDTVVIPFATPRNYLYELFSLYYM +>Sequence_1_ORF7 Translation of Sequence in frame 1, ORF 7, threshold 1, 3aa +VRL +>Sequence_1_ORF8 Translation of Sequence in frame 1, ORF 8, threshold 1, 40aa +SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV +>Sequence_1_ORF9 Translation of Sequence in frame 1, ORF 9, threshold 1, 29aa +FLVCTCSGASSLFTLFVYSSSFIFSMILI +>Sequence_2_ORF1 Translation of Sequence in frame 2, ORF 1, threshold 1, 3aa +FDA +>Sequence_2_ORF2 Translation of Sequence in frame 2, ORF 2, threshold 1, 27aa +NTFFCPYTDHSFPNGFTPTRNSCASTN +>Sequence_2_ORF3 Translation of Sequence in frame 2, ORF 3, threshold 1, 4aa +KRLA +>Sequence_2_ORF4 Translation of Sequence in frame 2, ORF 4, threshold 1, 7aa +SVTGLYS +>Sequence_2_ORF5 Translation of Sequence in frame 2, ORF 5, threshold 1, 5aa +ARLLP +>Sequence_2_ORF6 Translation of Sequence in frame 2, ORF 6, threshold 1, 32aa +SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL +>Sequence_2_ORF7 Translation of Sequence in frame 2, ORF 7, threshold 1, 46aa +YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG +>Sequence_2_ORF8 Translation of Sequence in frame 2, ORF 8, threshold 1, 11aa +YAVSLIFVVSS +>Sequence_2_ORF9 Translation of Sequence in frame 2, ORF 9, threshold 1, 32aa +NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV +>Sequence_2_ORF10 Translation of Sequence in frame 2, ORF 10, threshold 1, 1aa +F +>Sequence_3_ORF1 Translation of Sequence in frame 3, ORF 1, threshold 1, 90aa +SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE +DVVEEYNKYESLPPGLLITGYSCNTLRNTA +>Sequence_3_ORF2 Translation of Sequence in frame 3, ORF 2, threshold 1, 3aa +LSI +>Sequence_3_ORF3 Translation of Sequence in frame 3, ORF 3, threshold 1, 16aa +IIFPLLYVVGSSLIFL +>Sequence_3_ORF4 Translation of Sequence in frame 3, ORF 4, threshold 1, 13aa +QVFYCFRPQCSCS +>Sequence_3_ORF5 Translation of Sequence in frame 3, ORF 5, threshold 1, 9aa +VVLDNMRSV +>Sequence_3_ORF6 Translation of Sequence in frame 3, ORF 6, threshold 1, 37aa +SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF +>Sequence_3_ORF7 Translation of Sequence in frame 3, ORF 7, threshold 1, 8aa +YDFNLKQF diff -r d5c3794bd246 -r 27c43fb015f0 test-data/emboss_sixpack_out2.sixpack --- a/test-data/emboss_sixpack_out2.sixpack Mon Apr 23 13:04:47 2018 -0400 +++ b/test-data/emboss_sixpack_out2.sixpack Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,3 @@ - V R C L K Y L L L S L H R P Q F S * W L F1 F D A * N T F F C P Y T D H S F P N G F F2 @@ -6,11 +5,6 @@ gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| - caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa - T R H R F Y R R K D R C L G C N E * H S F6 - X E I G L I G E K T G V C V V T K R I A F5 - N S A * F V K K Q G * V S W L K G L P K F4 - Y T D * K F L C K H * L K A V G L E C Y F1 T P T R N S C A S T N * K R L A * S V T F2 @@ -18,11 +12,6 @@ tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| - atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg - * V S * F N K H L C * N F A T P R S H * F6 - K C R S S I R T C A S I S L P Q G L T N F5 - V G V L F E Q A L V L Q F R N A * L T V F4 - R F V * L S A S L A L I K G S F S L L W F1 G L Y S * A R L L P * S K V H F L Y F G F2 @@ -30,11 +19,6 @@ cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----| - gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc - R N T Y S L A D R A R I L P E N E R S Q F6 - G T Q I A S R T E Q G S * L N M K E V K F5 - P K Y L Q A R R K G Q D F T * K R * K P F4 - K T L W K N T T S T S L S P L V C * L L F1 R R C G R I Q Q V R V S P P W F A D Y W F2 @@ -42,11 +26,6 @@ aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 190 200 210 220 230 240 ----:----|----:----|----:----|----:----|----:----|----:----| - ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac - F V N H F F V V L V L R E G R T Q Q N S F6 - S S T T S S Y L L Y S D R G G P K S I V F5 - L R Q P L I C C T R T E G G Q N A S * Q F4 - D T V V I P F A T P R N Y L Y E L F S L F1 I Q L * Y P S Q H R V T I Y M N Y F P F F2 @@ -54,11 +33,6 @@ gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 250 260 270 280 290 300 ----:----|----:----|----:----|----:----|----:----|----:----| - ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa - S V T T I G K A V G R L * R Y S N N E R F6 - P Y L Q L V R R L V A Y S D I H I I K G F5 - I C N Y Y G E C C R T V I * I F * K G K F4 - Y Y M * * V R L * S S F S K S F T V F D F1 I I C S R F V F N L P L A S L L L F S T F2 @@ -66,11 +40,6 @@ tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 310 320 330 340 350 360 ----:----|----:----|----:----|----:----|----:----|----:----| - ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg - * * I Y Y T R R * D E K L L D K V T K S F6 - K N Y T T P E D K I K R * C T K * Q K R F5 - I I H L L N T K L R G K A L R K S N E V F4 - L N V H V L R L F W I I C G Q F N L R C F1 S M F M F L G C F G * Y A V S L I F V V F2 @@ -78,11 +47,6 @@ ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 370 380 390 400 410 420 ----:----|----:----|----:----|----:----|----:----|----:----| - gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca - R L T * T R L N N Q I I H P * N L R R Q F6 - G * H E H E * T T K S L I R D T * D E N F5 - E I N M N K P Q K P Y Y A T L K I K T T F4 - F F L K Y L F M V * F L V C T C S G A S F1 S S * N I Y S W F N F W F V L V Q G P V F2 @@ -90,11 +54,6 @@ ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 430 440 450 460 470 480 ----:----|----:----|----:----|----:----|----:----|----:----| - aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca - K K K F Y K N M T * N K T Q V Q E P A L F6 - N R R L I N I * P K I K P K Y K N L P W F5 - E E * F I * E H N L K Q N T S T * P G T F4 - S L F T L F V Y S S S F I F S M I L I * F1 H Y L L C L Y T A V L L F L V * F * F K F2 @@ -102,11 +61,6 @@ tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 490 500 510 520 530 540 ----:----|----:----|----:----|----:----|----:----|----:----| - agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt - E N N V R N T Y L L E K I K L I I K I * F6 - N M I * E T Q I C C N K * K * Y S K L K F5 - * * K S Q K Y V A T R K N K T H N * N L F4 - N N S N G Q K F1 T I L M V K X F2 @@ -114,21 +68,14 @@ aacaattctaatggtcaaaaa 550 560 ----:----|----:----|- - ttgttaagattaccagttttt - F L E L P * F F6 - F C N * H D F F5 - V I R I T L F F4 ############################## Minimum size of ORFs : 1 -Total ORFs in frame 1 : 10 -Total ORFs in frame 2 : 11 -Total ORFs in frame 3 : 8 -Total ORFs in frame 4 : 14 -Total ORFs in frame 5 : 12 -Total ORFs in frame 6 : 14 +Total ORFs in frame 1 : 9 +Total ORFs in frame 2 : 10 +Total ORFs in frame 3 : 7 -Total ORFs : 69 +Total ORFs : 26 ##############################