Tool for assigning putative transmembrane regions in a protein sequence

Reference: 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. http://www.ncbi.nlm.nih.gov/pubmed/9183525

SNNS.gbl file contains the neural network created with SNNS (Stuttgart Neural Network Simulator) http://www.ra.cs.uni-tuebingen.de/SNNS/ as explained in the paper above.

Within the same directory simply execute: make

transmem executable will be created.

transmem -w 12 -d Q9BTV4.fasta

This reads Q9BTV4.fasta file with a 12 window size and debugging option.

Lines starting with '#' are debug output and offers information about every residue.

Result lines include separated by tabs:

• IDs of FASTA entries
• a candidate transmembrane stretch of aas
• starting and ending positions within the query sequence.

#sp|Q9BTV4|TMM43_HUMAN@392|R->-1.1
#sp|Q9BTV4|TMM43_HUMAN@393|V->-1.1
#sp|Q9BTV4|TMM43_HUMAN@394|P->-1.1
#sp|Q9BTV4|TMM43_HUMAN@395|A->-1.1
#sp|Q9BTV4|TMM43_HUMAN@396|K->-1.1
#sp|Q9BTV4|TMM43_HUMAN@397|K->-1.1
#sp|Q9BTV4|TMM43_HUMAN@398|L->-1.1
#sp|Q9BTV4|TMM43_HUMAN@399|E->-1.1
sp|Q9BTV4|TMM43_HUMAN	GMFVGLMAFLLSFYL	34	49
sp|Q9BTV4|TMM43_HUMAN	AAGWMAMFMGLNLM	312	326
sp|Q9BTV4|TMM43_HUMAN	LVNIGLKAFAFCVATSLTLLTVAAGWLF	342	370
sp|Q9BTV4|TMM43_HUMAN	LWALLIAGLALVPIL	373	388