Answer to Question #42711 in Bioinformatics for umair ilyas

Question

The tasks for this assignments are very simple, but data retrieval for this assignment is little theoretical. You have to find out first any disease that are associated with inheritance or with other phenomena. Then you will find out these information

1. Name of the disease (Every student will work on two diseases. There are thousands of diseases so every one should perform on different diseases, If In case I found assignments on same diseases, then I will check the plagiarism first and then consider it otherwise that student will get zero mark).
2. Particular gene involved in this disease
3. Brief summary of this disease.
4. Retrieve all members of this gene and perform the question number "A" (See below) with this task only.
5. Retrieve sequences of this gene with different organisms as mentioned in number "B" (See below)
6. Perform Multiple sequence alignment.
7. Perform Phylogenetic analysis
8. Snapshot of your phylogram
9. Send me a document with all the related information i.e. all these eight tasks.

Total marks: 4 Marks

For your help, I'm explaining here one task (As I'm performing) that how to deal with this assignment.

Here I start:

I found Usher syndrome (USH) is the most frequent cause of deafness accompanied by blindness due to retinitis pigmentosa. Usher syndrome accounts for more than 50% of individuals who are both deaf and blind, about 18% of retinitis pigmentosa cases, and 3-6%of congenital deafness cases. Usher syndrome can be classified into three different clinical subtypes type I (USH I), type II (USH 2) and type III (USH3) and involves 12 loci (7 for USH1, 3 for USH2 and 2 for USH3). Seven genes have been identified, namely MYO7A, USH1C, CDH 23, PCDH15, SANS, USH2A and USH3A.

There are six major subclasses of the cadherin superfamily including protocadherin (i.e. PCDH15), almost all of which are expressed in the neuronal tissues, almost all of which are expressed in the neuronal tissues. A typical Protocadherin have up to seven to ten extracellular calcium binding domains, one transmembrane domian and a unique intracellular domain. Some Protocadherin genes occur in clusters, which may allow the generation of many isoforms. Protocadherin 15 is expressed in the sensory epithelia of the eye and ear.

Matter to think:
If we find out these specific genes from NCBI within five different species then we are able to find out their respective protein sequences and it would be quite easy to discover the conservation of these proteins among different organisms.

What to do:
You will be limited to one gene only and your tasks are as follows:
1) Find out the PCDH15 transcript that fully encode the Protocadherin protein and then retrieve the following information from this record:

(A)
a) Protein ID
b) Total number of amino acid residues
c) FASTA format of protein
d) All Calcium binding sites along with their residues and positions in sequence
e) Pathways for this current gene (any 2)
f) Genomic location of this gene

(B)
Retrieve the above mentioned information for these species:
• Macaca mulatta
• Homo sapiens
• Loxodonta Africana
• Mus musculus
• Felis catus
If you will not find any from the above then retrieve any five organisms having this gene sequence.