Programme in PERL programmieren

Hallo

Im Moment belegen ich den Kurs in der Uni Bioinformatik und soll in diesem Zuge einige Programme in BioPerl programmieren. Das Problem ist nur, dass ich auch nach Stunden langen davor sitzen, nicht weiß wie ich diese programmieren soll. Es wäre super wenn mir jemand helfen könnte.

Die Fragestellungen:

Aufgabe 1:

Write a program to use BLAST to compare each protein in one bacterial genome with those in another genome and decide which have homologues. Use this program with two appropriate genomes. When two proteins have similar sequences they are obviously homologues. You should consider appropriate parameters to define homology (e.g % amino acid identity) and how to cope with cases in which the proteins only show similarity in parts. Each of you should choose a different pair of related proteomes, which can be downloaded from the EBI genome server: e.g. Mycobacterium tuberculosis CDC15515 vs M. smegmatis MC2 155, Streptococcus pneumoniae R6 vs S. suis BM407, Streptomyces avermitilis MA-4680 vs S. griseus NBRC 13350.

Aufgabe2: 

There are many lipase/esterases present in GenBank most of which have only been defined by DNA sequence. One important family is the HSL-family of bacterial enzymes; they are so called because they have sequence similarities to the human hormone-sensitive lipase. Some of these enzymes have been characterised and they show a wide range of substrate preferences. It is believed that it might be possible to find good candidates for novel activities by looking at enzymes that differ in certain critical residues from those that have been characterised to date. These may be enzymes that differ at residues that are conserved in most of the other enzymes. It is also interesting to study subclasses of the enzymes that differ at particular residues (i.e. where the residue splits the enzymes into major classes). You will be given a PHYLIP format alignment of ca. 200 protein sequences and should write a program to help identify interesting enzymes.

Vielen Danke. 

anchen