Bioinformatics

3D structure of Collagen alpha 1 Alignment Guid tree Jalview Fasta Protein blast Phylogenetic tree Map viewer Conclusion Application

OUTLINE:-

COLLAGEN alpha1SUB-TOPIC:- Comparative study of collagen

alpha 1 between homo sapiens and macaca mulatta

Collagen alpha 1:-This is the most abundant collagen of the human body. It is present in scar tissue, the end product when tissue heals by repair. It is found in tendons, skin, artery walls, cornea, the endomysium surrounding muscle fibers, fibrocartilage, and the organic part of bones and teeth.

>tr|D3DSM7|D3DSM7_HUMAN Collagen, type VI, alpha 1, isoform CRA_a OS=Homo sapiens GN=COL6A1 PE=4 SV=1 MRAARALLPLLLQACWTAAQDEPETPRAVAFQDCPVDLFFVLDTSESVALRLKPYGALVD KVKSFTKRFIDNLRDRYYRCDRNLVWNAGALHYSDEVEIIQGLTRMPGGRDALKSSVDAV KYFGKGTYTDCAIKKGLEQLLVGGSHLKENKYLIVVTDGHPLEGYKEPCGGLEDAVNEAK HLGVKVFSVAITPDHLEPRLSIIATDHTYRRNFTAADWGQSRDAEEAISQTIDTIVDMIK NNVEQVCCSFECQPARGPPGLRGDPGFEGERGKPGLPGEKGEAGDPGRPGDLGPVGYQGM KGEKGSRGEKGSRGPKGYKGEKGKRGIDGVDGVKGEMGYPGLPGCKGSPGFDGIQGPPGP KGDPGAFGLKGEKGEPGADGEAGRPGSSGPSGDEGQPGEPGPPGEKGEAGDEGNPGPDGA PGERGGPGERGPRGTPGTRGPRGDPGEAGPQGDQGREGPVGVPGDPGEAGPIGPKGYRGD EGPPGSEGARGAPGPAGPPGDPGLMGERGEDGPAGNGTEGFPGFPGYPGNRGAPGINGTK GYPGLKGDEGEAGDPGDDNNDIAPRGVKGAKGYRGPEGPQGPPGHQGPPGPDECEILDII MKMCCEMQVRPHRPPVRAGQLREHWPAELRDCQGLRRQGHRPAEPGRAGQVRARAVVRGC GAVQPQPDAGAREPAQPQHPERAGAQGSHQEPAVDGGRHLHGGGPAVHAGPAAAAQPEQP HRPGHH

Homo sapiens (FASTA)

>tr|I0FP93|I0FP93_MACMU Collagen alpha-1(VI) chain OS=Macaca mulatta GN=COL6A1 PE=2 SV=1 MRAARALLPLLLQACWTAGQDEPETPRAVAFQDCPVDLFFVLDTSESVALRLKPYGALVD KVKSFTKRFIDNLRDRYYRCDRNLVWNAGALHYSDDVEIIQGLTRMPGDRDTLKSRVDAI KYFGKGTYTDCAIKKGLEQLLVGGSHLKENKYLIVVTDGHPLEGYKEPCGGLEDAVNEAK HLGVKVFSVAITPDHLEPRLSIIATDHTYRRNFTAADWGQSRDAEEVISQTIDTIVDMIK NNVEQVCCSFECQPARGPPGLRGDPGFEGERGKPGLPGEKGEAGDPGRPGDLGPVGYQGM KGEKGSRGEKGSRGPKGYKGEKGKRGIDGVDGVKGEMGYPGLPGCKGSPGFDGIQGPPGP KGDPGAFGLKGEKGEPGADGEAGRPGSSGPPGDEGEPGEPGPPGEKGEAGDEGNPGPDGA PGERGGPGERGPRGTPGTRGPRGDPGEAGPQGDQGREGPVGVPGDPGEAGPIGPKGYRGD EGPPGSEGARGAPGPAGPPGDPGLMGERGEDGPPGNGTEGFPGFPGYPGNRGPPGINGTK GYPGLKGDEGEAGDPGDDNNDIAPRGVKGAKGYRGPEGPQGPPGHPGPPGPDECEILDII MKMCSCCECKCGPIDLLFVLDSSESIGLQNFEIAKDFVVKVIDRLSRDELVKFEPGQSYA GVVQYSHSQMQEHVSLRSPSIRNVQELKEAIKNLQWMAGGTFTGEALQYTRDQLLPPSPN NRIALVITDGRSDTQRDTTPLNVLCSPGVQVVSVGIKDVFDFVPGSDQLNVISCQGLAPS QGRAGLSLVKENYAELLEDAFLKNVTAQICIDKKCPDYTCPIPFSSPADITILLDSSASV GSHNFDTTKRFAKRLAERFLMAGRTDPAHDVRVAVVQYSGTGQQRPERASLQFLQNYTAL ASAVDAMDFINDATDVNDALGYVTRFYREASSGAAKKRLLLFSDGNSQGATPAAIEKAVQ EAQRAGIEIFVVVVGRQVNEPHIRVLVTGKTAEYDVAYGERHLFRVPSYQALLRGVFHQT VSRKVALG

Macaca mulatta (FASTA)

ALIGNMENT

Protein blast

Dot matrix view

Jalview:-

Map viewer for homo sapiens

Map viewer for macaca mulatta

The rhesus(macaca mulatta) genome shares about 93 percent of its sequence with the human genome.

Conclusion:-

The rhesus is widely recognized as the best animal model for human immunodeficiency virus (HIV) infection.

It also serves as a valuable model for studying other human infectious diseases and for vaccine research.  

The rhesus macaque genome sequence enhances essential research in neuroscience, behavioral biology, reproductive physiology, endocrinology and cardiovascular studies.

Applications:-

https://www.google.co.in http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/Structure/MMD

B/mmdb.shtml http://www.uniprot.org/ http://blast.ncbi.nlm.nih.gov/Blast.cgi

Refferences:-