#DGpred ##Description Calculate the hydrophobicity (deltaG values) of protein sequences or peptides.

The web-server for dgpred is accessible at http://dgpred.cbr.su.se.

##Usage The main script for calculating the hydrophobicity is myscanDG.pl This script is modified from the original script DGpred_multi_scan.pl It can be used to calculate DG values by using either single sequence information or multiple sequence information. In the latter case, the path of NCBI blastpgp should be set.

Examples: In the subfolder "test"

• calculate DG values for the test sequence file 'test.fa' using single sequence information

  $ ../myscanDG.pl test.fa > test.dgvalue.single.txt

• calculate DG values for the test sequence file 'test.fa' based on multiple sequence alignment

  the blastpgp program should be located at /path/to/blast/bin/blastpgp
  /path/to/blastdb, e.g. /data/blastdb/nr
  /path/to/scampi-msa, is the scampi-msa from the modhmm package

`$ ../myscanDG.pl -multi test.fa -ncbidir /path/to/blast -blastdb /path/to/blastdb -scampipath /path/to/scampi-msa  > test.dgvalue.multi.txt`

• calculate DG values from the prf file

  $ ../myscanDG.pl test.prf > test.dgvalue.by.multi.prf.txt

##Other scripts

• analyze.pl analyze the delta G values of given a peptide e.g.

  $ ../analyze.pl YIYLGGAILAEVIGTTLMKF -o rst_pep.html

• calc_dG.pl calculate the delta G values given a list of peptides e.g.

  $ ../calc_dG.pl fragfile.txt -o rst_calc.html

• dG_predTM.pl predict the most hydrophobic regions given a protein sequence e.g.

  $ ../dG_predTM.pl test.fa -o rst_predTM.html