Compare human colon cancer gene MLH1 with other genes.

- To use ORF finder to translate DNA sequence to protein sequence in all reading frames. -
- To use blastn, blastp, CD search and blast 2 sequence programs for searching and comparison. -
-Deadline- 11/06/2001

1. Compare MLH1 (answer of assignment 2.6) and mutS (answer of 2.7) sequence.
   Ans. No significant alignment
   
   
2. Translate the above two gene sequences to protein sequences.
   Ans. MLH1 protein sequence --- mutS protein sequence
   
   
3. Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits.
   Ans.
   gi:13878583, MLH1_Mouse, DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1).
   gi:13591989, NP_112315, mismatch repair protein [Rattus norvegicus].
   gi:4557757, NP_000240, mutL homolog 1; mutL (E. coli) homolog 1 [Homo sapiens].
   gi:466462, AAA17374, human homolog of E. coli mutL gene product
   gi:604369, AAA85687.1, hMLH1 gene product.
   gi:12835158, BAB23172.1, putative [Mus musculus].
   gi:13543339, AAH05833.1, Similar to mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2) [Homo sapiens].
   gi:7304079, AAF59117.1, Mlh1 gene product [Drosophila melanogaster].
   gi:3192877, AAC19117.1, mutL homolog [Drosophila melanogaster].
   gi:460627, AAA16835.1, Mlh1p.
   
4. Compare human MLH1 protein with MLH1 in M. musculus, R. norvegicus and D. melanogaster. Give the pairwise alignment and % of sequence smility.
   Ans. pairwise alignment
   human MLH1 protein with
   MLH1 in M. musculus Identities = 651/760 (85%), Positives = 693/760 (90%), Gaps = 4/760 (0%)
   MLH1 in R. norvegicus Identities = 639/758 (84%), Positives = 684/758 (89%), Gaps = 3/758 (0%)
   MLH1 in D. melanogaster Identities = 335/751 (44%), Positives = 453/751 (59%), Gaps = 94/751 (12%)
   
5. Search the conserve domain (CD) for MLH1. Give the position of the CD, name of CD and Pfam ID number.
   Ans. pfam 01119
   Ans. Name DNA_mis_repair, DNA mismatch repair protein
   Ans. position 147~327
   
   
6. Show multiple alignment of MLH1 conserve domain with 5 sequences from the top of the CD alignment.
   Ans. multiple alignment