Soft­ware - TRFrag­C­alc

The free MAT­LAB script avail­able on this page can only run with MAT­LAB already in­stalled on your sys­tem (Win­dows, Linux, and Ma­cOS). Please visit MATLAB to get more in­form­a­tion about the pur­chase and in­stall­a­tion.

TRFragCalc - in silico prediction of terminal restriction fragments

Di­s­crip­tion:
The script TRFrag­C­alc was writ­ten in MAT­LAB (v.2.9.0.529 R2009b, MAT­LAB The Lan­guage of Tech­nical Com­put­ing, The Math­Works, Nat­ick, USA) to per­form in silico a ter­minal re­stric­tion frag­ment length poly­morph­ism (T-RFLP) ana­lysis of 16S rRNA gene se­quences. For more in­form­a­tion on T-RFLP, please read Liu et al. (1997). The sript provides an in­ter­act­ive pro­ced­ure for a step by step ana­lysis.
Be­fore start­ing TRFrag­C­alc (Step 0) the 16S rRNA gene se­quences of the SILVA database need to be pre­pared in ARB (Ludwig et al. 2004).
Ex­port all 16S rRNA gene se­quences (which are of in­terest) that match with 0 to 2 mis­matches the T-RFLP for­ward primer (e.g. 8-27F) and re­verse primer (e.g. 907R). Trun­cate the se­quences to the length spe­cified by the for­ward and re­verse primer us­ing the ed­itor in ARB.
The ex­port from ARB and im­port into MAT­LAB of 16S rRNA gene se­quences is via xml files. The data in the xml files are con­ver­ted into a MAT­LAB struc­ture form­ate (Step 1). Each xml file will be treated within the im­port pro­ced­ure as seper­ated branch which al­lows dur­ing the ana­lysis to dif­fer­en­ti­ate between bac­terial groups (e.g. Alphaproteobacteria vs. Gammaproteobacteria).
To en­sure that the res­ults of the in silico di­ges­tion are com­par­able between the se­quences TRFRag­C­alc pre­pares the se­quences (Step 2) by (i) ex­clud­ing se­quences with am­bi­gu­ities, (ii) ex­clud­ing se­quences that do not match the for­ward and re­verse primer, and (iii) re­mov­ing the 5' and 3' over­hang.
For in silico T-RFLP ana­lysis (Step 3) the skript provides the op­por­tun­it­ies to de­term­ine (i) the length of the 16S rRNA gene se­quences, (ii) the length of the in silico ter­minal re­stric­tion frag­ments (iTRF), and (iii) the G+C and A+G con­tent of each se­quence.
Fi­nally (Step 4), the sript en­ables the pos­sib­il­ity to search all 16S rRNA gene se­quences that be­long to a iTRF of spe­cified length, or to de­term­ine the T-RFLP pat­tern of a bac­terial group.


The zipped folder TRFrag­C­al­c_v_1.1 in­cludes the files of the MAT­LAB script.
The zipped folder SILVA_rel102_827F_907R_2MM in­cludes xml files which rep­res­ent the pre­pared data­base of 16S rRNA gene se­quences of all bac­terial phyla.

Last up­dated: R.L. Hahnke, 20 Au­gust 2013