Hi Eddie, The sign indicates stranded-ness but the coordinates always refer to the forward strand.
To obtain the correct sequence, you would extract the subsequence with the absolute value of the coordinates, then reverse complement it if the coordinates are negative. Best, -Aaron On Sat, 2014-04-12 at 03:26 +1000, Eddie wrote: > Hello everyone, > I have a question about negative values on backbone files. > My question is: is the negative value the coordinate to the > complementary strand 5'->3'? Or it is the absolute value of > complementary strand 3'->5'? > > Lets say i have a sequence that ranges from 1 to 100 nt. If my > backbone file points -20 to -30 it is equivalent to the region 70 to > 80 of the complementary strand? > > I want to know because i'm crossing coordinates with gbk files, in > which the complementary is counted from the end to the beggining > (absolute value 5'->3'), to check if there is overlaps and i'm very > confused on how it works... > > Example: > 5' ATCATCGCAT '3 > '3 TAGTAGCGTA '5 > > If the backbone points -2 to -4 it's "AGTA" (absolute value 3'->5') or > it is "TGCG" (absolute value 5'->3'). > In other words to get the same coordinates of a gbk file i have to > subtract the absolute value to the genome lenght in order to obtain > the real coordinate? > > Thanks in advance, > Eddie Imada > Eddie Imada > > Mestrando em Genética e Biologia Molecular - UEL > > Laboratório de Genética de Microorganismos > > Cel: (43) 9973-3416 > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
