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Immunological prediction tools (MHC/TAP/Proteasome)


Most of the specific tools can be found by typing
ls -l /home/projects/projects/vaccine/bin


epitope2protein.pl - find proteins corresponding to epitopes
#
# See test file
#
cat test.fasta
>HLA-DPA1.0102 19 Example_for_Ligand
ADEKKFWGKYLYEIARRHP
>HLA-DPA1.0102 17 Example_for_Ligand
GEPLSYTRFSLARQVDG
#
# Find epitopes in NCBI non redundant database (nr) (from the database blast uses) - 
you can search for the corresponding proteins at the NCBI website
#
fastacmd -d nr -D | /home/ibiology1/projects/vaccine/bin/fasta2tab.gawk | 
epitope2protein.pl -f test.fasta -s -a 
#
# Find epitopes in swissprot/trembl (from the compressed fasta files)
# 
gunzip -c /home/projects/projects/vaccine/data/sp/2004/*.fas.Z |
 /home/ibiology1/projects/vaccine/bin/fasta2tab.gawk | epitope2protein.pl -f test.fasta -s -a 


There are some exceptions especially those programs which have been installed centrally to be part of a webserver. These include

CPHmodels - Homology modelling
/usr/cbs/bio/src/cm-2.0/cm2.pl -i fastafile


ProtFun - Protein function prediction: Sorry still in Danish
protfun -q A2.uniq.single.human.fasta > A2.uniq.single.human.fun

-q betyder ingen kommentarer om hvordan processen skrider fremad .fun 
filen er den lange med kategorier for hvert protein

Hvis du kun vil have den korte hvor der kommer en linie med 35 tal 
efterfulgt af et proteinnavn saa skal du bruge pf2howlin scriptet, der 
ligger i /home/genome6/peder/bin/

pf2howlin A2.uniq.single.human.fun > A2.uniq.single.human.fun.howlin

Eller man kan kombinere dem:

protfun -q A2.uniq.single.human.fasta | pf2howlin > 
A2.uniq.single.human.fun.howlin

Protfun bytter rundt paa raekkefxlgen af proteinerne og nogle af dem 
tager den ikke af ukendte grunde. Protfun har en nedre 
stxrrelsesgraense paa 50 aa og en xvre paa et sted mellem 3050 og 3100 
aa.