Hi good day. Sorry, I have a silly doubt, if someone could help me I would really appreciate it. You see, I'm using EMBOSS's transeq tool (something new for me) to translate an ORF file. When translating the 6 different reading frames and wanting to find which would be the longestORF and therefore the one indicated to use in later steps. But it turns out that in the translation files, there are lines with the legend "(REVERSE SENSE)" even when using the command to indicate that I wanted to translate the reading frame 1 (which I understand is the one that starts from the first amino acid and this it is not read in reverse) and in the files resulting from using the commands to obtain the frames in reverse (4, 5 and 6) there are both, lines with "(REVERSE SENSE)" and with absence of this legend.
This is how the content of translation archives looks like
>Something1_1_17_6 [756 - 785] ILRRTLPTFL >Something1_1_18_6 [789 - 818] *FVILLQCTX >Something1_1_19_6 [737 - 826] LFTDL*FFCNVHIRF*DGLFQHFFI*IFNX >Something1_1_20_6 [814 - 740] (REVERSE SENSE) *RFR*RNVGRVRLKI*CVHCRRITX >Something1_1_21_6 [732 - 685] (REVERSE SENSE) HWMRRML*I*AAI*PV >Something1_1_22_6 [736 - 671] (REVERSE SENSE) HG*SNIG*GGCCEYELPYDQFX
To generate it I used the comand
transeq imputfile outputfilename.pep -frame=-3 , which is supposed to generate the third reverse translation (frame 6)
Oh, if you think this is not the best way to find the longestORF and want to recommend something else, I would greatly appreciate any input. :D
Thank you very much for taking the time to read and thank you very much in advance to those who can answer my question. Have a nice day!