Conceptualizing Combined Knowledge Of Computer Sciences Biology Essay

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INTRODUCTION:

BIOINFORMATICS is a field of science where conceptualizing combined knowledge of computer sciences, information technology and biology. This is software technology used for storing the biological databases and retrieving the information about proteomic and genomic genetic interactions in large scale. The simplest way to describe BIOINFORMATICS is shotgun marriage between biology and information technology.

PARK2 gene is the largest gene in human beings. For retrieving information about park2 gene various bioinformatics tools are used. This gene belongs to the protein group called E3protien-ubiquitin ligases. Mutation in this park2 gene causes Parkinson's diseases .In human's parkin protein is encoded by this park2 gene. The main function of this parkin protein is unknown. Parkin protein breaks down the unwanted proteins by the molecules ubiquitin and plays a major role in cell machinery.

METHODS:

HUGO GENE NOMENCLATURE COMMITTEE.

This is a search engine which searches all the databases and gives all the information regarding the given gene. For each and every gene their will be a common name, scientific name and abbreviated symbol. All these approved genes with all those information's are stored in HUGO .We can get all the required information about the genes and their functions along with their scientific references of the given gene.

(http://www.genenames.org/)

OMIM:

ONLINE MENDELIAN INHERITANCE IN MAN

It gives all the data regarding phenotypic and genotypic genetic disorders in human genes. All the genetic diseases which are inherited or heritable primarily focus by OMIM. Mendelian Inheritance gives all the references about the transfer gene characters from one generation to the other generations. All the information regarding the conserved domains present in the gene can obtained by this OMIM.

OMIM Morbid Map:

It gives all the diseases lists and corresponding cytogenetic locations. We can get the list of genes that causes the same diseases due to mutations.

PUBMED:

The Pubmed is the database which is used for searching the literature in biomedical sciences and life sciences. All the articles, journals and books regarding biosciences are available in these databases.

ENSEMBLE:

It is a Bioinformatics web based tool which maintains the automatic annotations of the genomes and details of eukaryotic genomes. For all the large genomes it arranges biological information. For WELCOME TRUST SANGER INSTITUE (WTSI) and EUROPEAN BIOINFORMATICS INSTITUE (EBI) Ensemble is the joint venture.

BLAST:

BASIC LOCAL ALINGMENT SEARCH TOOL.

Wu-BLAST: - Washington university Basic Local Alignment Search Tool.

BLAST is a search tool which gives all the information regarding protein and Nucleotide sequences. It gives the sequences similarity and functional information about the structure and the sequences. This is an algorithm for comparing different biological sequences information such as nucleotide of DNA sequences and amino acids of different proteins.

EMBOSS TRANSEQ:

It translates all the nucleic acid sequences into the corresponding peptide sequences. It translates in all the six frames or three forward, three reverse frames.

Db clustal:

It gives all the corresponding complex sequences information and the global alignment. Db clustal combines both global and local alignments into a single program

RESLUTS AND DISCUSSIONS:

1) The mutations in the chosen gene cause PARKINSON'S DISEASES.

The other diseases that caused by park2 gene are OVARIAN CANCER, LUNG CANCER,LEPROSY,DEMENTIA,SPINAL MUSCULAR ATROPHY.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

2) The original references for the park2 gene in Harvard and near Harvard format is Di Fonzo+park2+mutation in GLY 504 ARG.

Di Fonzo, A., Chien, H. F., Socal, M., Giraudo, S., Tassorelli, C., Iliceto, G., Fabbrini, F., Marconi, R., Fincati, E., Abbruzzese, F., Marini, P., Squitieri, F., and 14 others ATP13A2 missense mutations in juvenile parkinsonism and young onset Parkinson disease. Neurology 68: 1557-1562, 2007. [PubMed: 17485642]

3) The other genes that cause this disease or similar diseases are PRKN, PDJ, LPRS2, LRRK2, and PARK8. These results are retrieved from this given website.

Disorder

Symbol(s)

OMIM

Location

Parkinson disease, juvenile, type 2, 600116 (3)

PRKN, PARK2, PDJ, LPRS2

602544

6q25.2-q27

Parkinson disease-8, 607060 (3)

LRRK2, PARK8

609007

12q12

Parkinsonism-dystonia, infantile, 613135 (3)

SLC6A3, DAT1

126455

5p15.3

Paroxysmal extreme pain disorder, 167400 (3)

SCN9A, NENA, PN1, FEB3B

603415

2q24

Paroxysmal kinesigenic choreoathetosis (2)

PKC, DYT10

128200

16p11.2-q12.1

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM.

4) The symbol that is used in the beginning of the title of the FASTA sequences is ">".

5) The chosen mutation of park2 gene is not the know functional domain of the protein.

For the park2 gene the mutation is at GLY 504 ARG.

This conserved domain of the park2 gene obtained from the unigene

6) Nucleotide alignment results:

Normal

1501 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTGGGGGGCAAGCTGCAGCT

1467 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTGGGGGGCAAGCTGCAGCT

489 --R--Q--G--I--F--C--I--H--P--L--R--I--N--L--G--G--K--L--Q-L

Mutated

1501 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTGGGGGGCAAGCTGCAGCT

1467 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTAGGGGGCAAGCTGCAGCT

489 --R--Q--G--I--F--C--I--H--P--L--R--I--N--L--A--G--K--L--Q-L

The above sequences shows that the mutation from G to A.

EMBOSS ALINGMENT:

EMBOSS_001 1 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTGGGGGGCA 50

||||||||||||||||||||||||||||||||||||||||||||||||||

EMBOSS_001 1 GAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAACCTGGGGGGCA 50

EMBOSS_001 51 AGCTGCAGCTGAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAAC 100

||||||||||||||||||||||||||||||||||||||||||||||||||

EMBOSS_001 51 AGCTGCAGCTGAGACAGGGCATTTTCTGCATCCACCCACTGCGCATCAAC 100

EMBOSS_001 101 CTGGGGGGCAAGCTGCAGCT 120

||.|||||||||||||||||

EMBOSS_001 101 CTAGGGGGCAAGCTGCAGCT 120

7) Protein alignment results:

The above mRNA sequences the translated protein sequences are retrieved by using this web link.

http://www.ebi.ac.uk/Tools/emboss/transeq/

NORMAL

>EMBOSS_001_1

ETGHFLHPPTAHQPGGQAAAETGHFLHPPTAHQPGGQAAA

>EMBOSS_001_2

RQGIFCIHPLRINLGGKLQLRQGIFCIHPLRINLGGKLQL

>EMBOSS_001_3

DRAFSASTHCASTWGASCS*DRAFSASTHCASTWGASCSX

MUTATED

>EMBOSS_001_1

ETGHFLHPPTAHQPGGQAAAETGHFLHPPTAHQPRGQAAA

>EMBOSS_001_2

RQGIFCIHPLRINLGGKLQLRQGIFCIHPLRINLGGKLQL

>EMBOSS_001_3

DRAFSASTHCASTWGASCS*DRAFSASTHCAST*GASCSX

EMBOSS ALINGMENT:

The above peptide sequences are aligned using the following web link

http://www.ebi.ac.uk/Tools/emboss/align/

#####################################

# Program: needle

# Rundate: Fri 26 Nov 2010 12:18:54

# Commandline: needle

# [-asequence] /ebi/extserv/old-work/needle-20101126-1218545634.input.1

# [-bsequence] /ebi/extserv/old-work/needle-20101126-1218545634.input.2

# -outfile /ebi/extserv/old-work/needle-20101126-1218545634.output

# -gapopen 10.0

# -gapextend 0.5

# -datafile EBLOSUM62

# -sprotein1

# -sprotein2

# -auto

# Align_format: srspair

# Report_file: /ebi/extserv/old-work/needle-20101126-1218545634.output

########################################

#=======================================

#

# Aligned_sequences: 2

# 1: EMBOSS_001_3

# 2: EMBOSS_001_3

# Matrix: EBLOSUM62

# Gap_penalty: 10.0

# Extend_penalty: 0.5

#

# Length: 40

# Identity: 39/40 (97.5%)

# Similarity: 38/40 (95.0%)

# Gaps: 0/40 ( 0.0%)

# Score: 197.0

#

#

#=======================================

EMBOSS_001_3 1 DRAFSASTHCASTWGASCS*DRAFSASTHCASTWGASCSX 40

||||||||||||||||||| |||||||||||||.|||||

EMBOSS_001_3 1 DRAFSASTHCASTWGASCS*DRAFSASTHCAST*GASCSX 40

#---------------------------------------

#---------------------------------------

WU-BLAST:

BLAST the mutant protein sequences into http://www.ebi.ac.uk/blast2/index.html

Before running the blast make sure to change the settings to uniprot /swissprot. Check them all and run db clustal.

http://www.ebi.ac.uk/Tools/services/web/blastresult.ebi?tool=wublast&jobId=wublast-I20101126-142340-0059-26630864&context=protein

Db clustal:

These results show that the protein sequence conserves in all the species.

It shows all the species aligns with all the hits together.

Sequence ------------------------------------------------------------

Q8PI13_XANAC SGAMLPLSSLAIYAAYKETREVAEQRTHLRQRERRLRLEQAALQSA--LGTAAPSGAANA 356

D4T4K7_9XANT SGAMLPLSSLAIYAAYKETREVAEQRTHLRQQERRLRAEQATLQSA--LGTTAPAGAANA 193

D4SZ81_9XANT SGAMLPLSSLAIYAAYKETREVAEQRTHLRQQERRLRAEQATLQSA--LGTTAPAGAANA 284

Q6N098_HUMAN ------AETVTVTVLFREEGRRNQCRGRLSGVDRRCPQLTGSMTLE--EWKLRQSRDVRV 56

B0CFJ1_ACAM1 ------GMDAAITKFFGVELEWNVKSQILETYLGEQPIGTSMIVET--GHPQHPYLAHTP 107

C0ZEZ0_BREBN -----RFFHPRSKTFRRLPFSGVSFTPEWSKYNRLRPTVHEPIAQAGILGKIKEACEQAG 100

B2IZI0_NOSP7 ------GIDAAIR-FFGRPLMARVQQRILEDYLGEQPVGTSMIVET--GHHKHPFLAHTP 105

A8NKM6_BRUMA -------------------------MQQQEKLPTHNPTVQNTNPSS--HHLYPPNAHHPR 33

Q3BQL7_XANC5 SGAMLPLSSLAIYAAYKETREVAEQRTHLRQQERRLRAEQATLQSA--LGTTAPAGAANA 339

Q6K8C0_ORYSJ -------MQTTHLKNLKLPHRLKILCPNFGSPQCKWPHGHPPPLHNPLHFLHPPTLASLP 53

Glycine G is the smallest amino acid having any charge, But Arginine(R) is a positive charge amino acid. Mutation in Park2 gene is not conserved in all the species.

Conclusion:

The mutation of the park2 gene is analysed by using various bioinformatics tools like to HUGO, OMIM, ENSEMBEL, EXPASY, PUBMED, WU-BLAST2, NCBI, and DBCLUSTAL. The mutation in park2 gene is carried out and it is observed in all the species. Glycine G is mutated to Arginine A at codon 504.The protein sequences was conserved through out the species is shown by the Db clustle alignment. The mutations in this Park2 gene cause Parkinson's diseases due to mutations in the amino acid residues.

11) Complementary coding DNA sequences is

3' T T C T T A C T G T A T A G G 5'

The mRNA sequences from the codogenic strand

3'U U C U U A C U G U A U A G G 5'

D) 5'3' Frame 1

aagaatgacatatcc

K  N  D  I  S  

3'5' Frame 1

ggatatgtcattctt

G  Y  V  I  L  

E) http://expasy.org/cgi-bin/dna_aa

The above website is used to find frame1 translation.

 

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