Question

ATGGTACTATCTCCTGAGTGCTGCAAGTTGTAACGGGCACCGCTGAGCCTGTTTCCCTTTGGAGCACTTC

TTATCTAGAAGCAGTGTTTAGTTTCTTCCAAACTGGGCCACTTCGTCCACCTACTCTGTTCTGAGTAAGG

AAACAGCCTCCAAGCATCAGCAGAGCCCAGATGAGCACGGGCCGCGGAGCCGCTTAGCAGTCTCCCGGGA

CCCAGCTCCGGAGGAGCCGCAAGCATGCACCCTGGGTTGTGGCTGCTCCTGGTTACGTTGTGCCTGACCG

AGGAACTGGCAGCAGCGGGAGAGAAGTCTTATGGAAAGCCATGTGGGGGCCAGGACTGCAGTGGGAGCTG

TCAGTGTTTTCCTGAGAAAGGAGCGAGAGGACGACCTGGACCAATTGGAATTCAAGGCCCAACAGGTCCT

CAAGGATTCACTGGCTCTACTGGTTTATCGGGATTGAAAGGAGAAAGGGGTTTCCCAGGCCTTCTGGGAC

CTTATGGACCAAAAGGAGATAAGGGTCCCATGGGAGTTCCTGGCTTTCTTGGCATCAATGGGATTCCGGG

CCACCCTGGACAACCAGGCCCCAGAGGCCCACCTGGTCTGGATGGCTGTAATGGAACTCAAGGAGCTGTT

GGATTTCCAGGCCCTGATGGCTATCCTGGGCTTCTCGGACCACCCGGGCTTCCTGGTCAGAAAGGATCAA

AAGGTGACCCTGTCCTTGCTCCAGGTAGTTTCAAAGGAATGAAGGGGGATCCTGGGCTGCCTGGACTGGA

TGGAATCACTGGCCCACAAGGAGCACCCGGATTTCCTGGAGCTGTAGGACCTGCAGGACCACCAGGATTA

CAAGGTCCTCCAGGGCCTCCTGGTCCTCTTGGTCCTGATGGGAATATGGGGCTAGGTTTTCAAGGAGAGA

AAGGAGTCAAGGGGGATGTTGGCCTCCCTGGCCCAGCAGGACCTCCACCATCTACTGGAGAGCTGGAATT

CATGGGATTCCCCAAAGGGAAGAAAGGATCCAAGGGTGAACCAGGGCCTAAGGGTTTTCCAGGCATAAGT

GGCCCTCCAGGCTTCCCGGGCCTTGGAACTACTGGAGAAAAGGGAGAAAAGGGAGAAAAGGGAATCCCTG

GTTTGCCAGGACCTAGGGGTCCCATGGGTTCAGAAGGAGTCCAAGGCCCTCCAGGGCAACAGGGCAAGAA

AGGGACCCTGGGATTTCCTGGGCTTAATGGATTCCAAGGAATTGAGGGTCAAAAGGGTGACATTGGCCTG

CCAGGCCCAGATGTTTTCATCGATATAGATGGTGCTGTGATCTCAGGTAATCCTGGAGATCCTGGTGTAC

CTGGCCTCCCAGGCCTTAAAGGAGATGAAGGCATCCAAGGCCTACGTGGCCCTTCTGGTGTCCCTGGATT

GCCAGCATTATCAGGTGTCCCAGGAGCCCTAGGGCCTCAGGGATTTCCAGGGCTGAAGGGGGACCAAGGA

AACCCAGGCCGTACCACAATTGGAGCAGCTGGCCTCCCTGGCAGAGATGGTTTGCCAGGCCCACCAGGTC

CACCAGGCCCACCTAGTCCAGAATTTGAGACTGAAACTCTACACAACAAAGAGTCAGGGTTCCCTGGTCT

CCGAGGAGAACAAGGTCCAAAAGGAAACCTAGGCCTCAAAGGAATAAAAGGAGACTCAGGTTTCTGTGCT

TGTGACGGTGGTGTTCCCAACACTGGACCACCCGGGGAACCAGGCCCACCTGGTCCATGGGGTCTCATAG

GCCTTCCAGGCCTTAAAGGAGCCAGAGGAGATCGAGGCTCTGGGGGTGCACAGGGCCCAGCAGGGGCTCC

AGGCTTAGTTGGGCCTCTGGGTCCTTCAGGACCCAAAGGAAAGAAGGGGGAACCAATTCTCAGTACAATC

CAAGGAATGCCAGGAGATCGGGGTGATTCTGGCTCCCAGGGCTTCCGTGGTGTAATAGGAGAACCAGGCA

AGGACGGAGTACCAGGTTTACCAGGTCTGCCAGGCCTTCCGGGTGATGGTGGACAGGGCTTCCCAGGTGA

AAAGGGGTTACCTGGACTTCCTGGTGAAAAAGGCCATCCTGGTCCACCTGGCCTCCCAGGAAATGGGTTA

CCAGGACTTCCTGGACCCCGTGGGCTTCCTGGAGATAAAGGCAAGGATGGATTACCGGGACAACAAGGCC

TTCCCGGATCTAAGGGAATCACCCTGCCCTGTATTATTCCTGGGTCATACGGTCCATCAGGATTTCCAGG

CACTCCCGGATTCCCAGGCCCTAAAGGGTCTCGAGGCCTCCCTGGGACCCCAGGCCAGCCTGGGTCAAGT

GGAAGTAAAGGAGAGCCAGGGAGTCCAGGATTGGTTCATCTTCCTGAATTACCAGGATTTCCTGGACCTC

GTGGGGAGAAGGGCTTGCCTGGGTTTCCTGGGCTCCCTGGAAAAGATGGCTTGCCTGGGATGATTGGCAG

TCCAGGCTTACCTGGTTCCAAGGGAGCCACTGGTGACATCTTTGGTGCTGAAAATGGTGCTCCGGGGGAA

CAAGGCCTACAAGGATTAACAGGGCACAAAGGATTTCTTGGAGACTCTGGCCTTCCAGGACTCAAGGGTG

TGCACGGGAAGCCTGGCTTACTAGGCCCCAAAGGTGAGCGGGGCAGCCCTGGGACACCAGGACAGGTGGG

ACAGCCAGGCACCCCAGGATCTAGTGGTCCATATGGCATCAAGGGCAAATCTGGGCTCCCAGGAGCACCA

GGCTTCCCAGGCATCTCAGGACATCCTGGAAAGAAAGGAACAAGAGGCAAGAAAGGTCCTCCTGGATCAA

TTGTAAAGAAAGGGCTGCCAGGGCTAAAAGGCCTTCCTGGAAATCCAGGCCTAGTAGGACTGAAAGGAAG

CCCAGGCTCTCCAGGGGTCGCTGGGTTGCCAGCCCTCTCTGGACCCAAGGGAGAGAAGGGGTCTGTTGGA

TTCGTAGGTTTTCCAGGAATACCAGGTCTGCCTGGTATTTCTGGAACAAGAGGATTAAAAGGAATTCCAG

GATCAACTGGAAAAATGGGACCATCTGGACGCGCTGGTACTCCTGGTGAAAAGGGAGACAGAGGCAATCC

GGGGCCAGTCGGAATACCTAGTCCAAGACGTCCAATGTCAAACCTTTGGCTCAAAGGAGACAAAGGCTCT

CAAGGCTCAGCCGGATCCAATGGATTTCCTGGGCCAAGAGGTGACAAAGGAGAGGCTGGTCGACCTGGAC

CACCAGGCCTACCTGGAGCTCCTGGCCTCCCAGGCATTATCAAAGGAGTTAGTGGAAAGCCAGGGCCCCC

TGGCTTCATGGGAATCCGGGGTTTACCTGGCCTGAAGGGGTCCTCTGGGATCACAGGTTTCCCAGGAATG

CCAGGAGAAAGTGGTTCACAAGGTATCAGAGGGTCGCCTGGACTCCCAGGAGCATCTGGTCTCCCAGGCC

TGAAAGGAGACAACGGCCAGACAGTTGAAATTTCCGGTAGCCCAGGACCCAAGGGACAGCCTGGCGAATC

TGGTTTTAAAGGCACAAAAGGAAGAGATGGACTAATAGGCAATATAGGCTTCCCTGGAAACAAAGGTGAA

GATGGAAAAGTTGGTGTTTCTGGAGATGTTGGCCTTCCTGGAGCTCCAGGATTTCCAGGAGTTGCCGGCA

TGAGAGGAGAACCAGGACTTCCAGGTTCTTCTGGTCACCAAGGGGCAATTGGGCCTCTAGGATCCCCCGG

ATTAATAGGACCCAAAGGCTTCCCTGGATTTCCTGGTTTACATGGACTGAATGGGCTTCCGGGCACCAAG

GGTACCCATGGCACTCCAGGACCTAGTATCACCGGTGTGCCTGGGCCTGCTGGTCTCCCTGGACCCAAAG

GAGAAAAAGGATATCCAGGAATTGGCATCGGAGCTCCAGGGAAGCCGGGCCTGAGAGGGCAAAAAGGTGA

TCGAGGTTTCCCAGGTCTCCAGGGCCCTGCTGGTCTCCCCGGTGCCCCAGGCATCTCCTTGCCCTCACTC

ATAGCAGGACAGCCTGGTGACCCCGGGCGACCAGGCCTAGATGGAGAACGAGGCCGCCCAGGCCCCGCTG

GACCCCCAGGTCCCCCTGGGCCATCCTCGAATCAAGGCGACACCGGAGACCCTGGCTTCCCTGGAATTCC

AGGTTTTTCTGGCCTCCCTGGAGAGCTAGGACTGAAAGGCATGAGAGGTGAGCCTGGCTTCATGGGGACT

CCAGGCAAGGTTGGGCCACCTGGAGACCCAGGATTTCCCGGAATGAAGGGGAAGGCAGGGGCAAGAGGCT

CTTCTGGCCTCCAAGGTGATCCTGGACAAACACCAACTGCAGAAGCTGTCCAGGTTCCTCCTGGACCCTT

GGGTCTACCAGGGATCGATGGCATCCCTGGCCTCACTGGGGACCCTGGGGCTCAAGGCCCTGTAGGCCTA

CAAGGCTCCAAAGGTTTACCTGGCATCCCCGGTAAAGATGGCCCCAGTGGGCTCCCAGGCCCACCTGGGG

CTCTTGGTGATCCTGGTCTGCCTGGACTGCAAGGCCCTCCAGGATTTGAAGGAGCTCCAGGGCAGCAAGG

CCCCTTCGGGATGCCTGGAATGCCTGGCCAGAGCATGAGAGTGGGCTACACGTTGGTAAAGCACAGCCAG

TCGGAACAGGTGCCCCCGTGTCCCATCGGGATGAGCCAGCTGTGGGTGGGGTACAGCTTACTGTTTGTGG

AGGGGCAAGAGAAAGCCCACAACCAGGACCTGGGCTTTGCTGGCTCCTGTCTGCCCCGCTTCAGCACCAT

GCCCTTCATCTACTGCAACATCAACGAGGTGTGCCACTATGCCAGGCGCAATGATAAATCTTACTGGCTC

TCCACTACCGCCCCTATCCCCATGATGCCCGTCAGCCAGACCCAGATTCCCCAGTACATCAGCCGCTGCT

CTGTGTGTGAGGCACCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCGCAGTGCCCCCT

GGGCTGGCGCAGCCTCTGGATTGGGTACTCTTTCCTCATGCACACTGCCGCTGGTGCCGAGGGTGGAGGC

CAGTCCCTGGTCTCACCTGGCTCCTGCCTAGAGGACTTTCGGGCCACTCCTTTCATCGAATGCAGTGGTG

CCCGAGGCACCTGCCACTACTTTGCAAACAAGTACAGTTTCTGGTTGACCACAGTGGAGGAGAGGCAGCA

GTTTGGGGAGTTGCCTGTGTCTGAAACGCTGAAAGCTGGGCAGCTCCACACTCGAGTCAGTCGCTGCCAG

GTGTGTATGAAAAGCCTGTAGGGTGGCACCTGCCACTCTGCCCCTTGCCCTCCCCTGCCCCTCACAACAG

TCACCTCACAAACCTGAATGGTCTGAAGAAGGAAGGCCTGAGCCCCTTTGCCTGTCAAGTTGTACATTGG

AGTCTCATTTGGGCTAGACTACCGGACACTCGTCACCCCAGCCCTCGGGTCCATAGAGATGAGCCCACCC

TGCTGAGATCTGCTGTCCTGTTTCTGTCAAGCTGGTGCTACTGTTTGATTTGGATGATTGTGTGACTATT

CATGGCTACCTCAGAAAGATTTGATGGGCCACAACTGTCTTAGACTGCTAGCTTTCTCCTTACCGTCTTG

ATCGGAAAGCTCTTCCGAATCGCTAATCAGTCATTTCTTCATGTACAGAGGTCAGCACACATTATTTGGC

TTAAACCAGAACCCAGTGTTTCCACACTTAAATTCTCTAACCGAATATTCATGGATGGCTCAAGTCTGCA

CAGAGCAAGTCCTCACTCTTCAAGGAGGCCCACTGTGTCTAGGCAGGCAAGAGAATTGAAATGAGGTGCC

ACCCAGTAGCCCAGAGTGAGCTTTAGCTCTAGAATGAGCAAGACTGGGCCCCACATGGCTTAGAGAGGCT

TGAAGGCCAGCAGCTGGGTTGGGGGTGGTGGTCATTAATGGCATATGGTCCTAGACAAACCATCTCCTCC

TTGCCGGCTCCCCCTCCAGCCAGAGACAGAGGATGTGGCCTGGTTCAAAGTAAAGCAGAGGATGCAACAA

ATGTGGCCAAGCTATCAAAGGAAATGAGAATGACAGCCTTTTTTCCTGGGCCAGAAGTAGAGGGGGTGGG

TGCGTAGGATGTGTGAGTTTTGCTTTTGACTCCAGGAACAAAAAGGTAAATCCCACATCCCAGTTTCTCA

GAAGTCCCTGTTTATTCCAATTGCCATCAGATGTGTGCAATGTGGCAAACTGAAGCTGCACAGTGTTGGT

TTCCTTGTATTCTGAGGATGTTAAAGACTTTGTTAAATGGTTATCCAATTGCTCTTTCACAGGTAGCCTA

TTAAACTATTTTAATATGTTTTTTTAAACCTCATAAAAATCTAGCACACTCTTCTCTTGAGCAGTTAGCA

GACCACCG

What are the different types of blast? What are their functions?

What is our protein?

Why did we pick this and not the others?

What web-tool can we use to find the function of this protein?

How many disulfide bonds are there?

What program will you use to find the information below?

What is the proteins accession number?

What does PDB stand for?

What is the PDB number for collagen?

What webtool can you use for macromolecular visualization?

What method was used to create this molecular model?

What are the ligands?

How many water molecules are there?

Post a snip of the parts of collagen that are polar?

Name one application in which bioinformatics is useful:

Answer 1

Basic Local Alignment Search Tool (BLAST) is an algorithm and program for comparing primary biological sequence information such as the nucleotides of DNA , RNA sequences or the amino-acid sequences of proteins referred as a query with the information provided in the databases. There are different classes or options of BLAST search , these are:

blastn: It searches nucleotides against nucleotides i.e when you put the DNA/nucleotide sequences as your query it will provide you the sequence match with the reference sequence in the database. For nucleotides there is a faster version of blastn called as megablast.

blastp: It searches proteins against proteins

blastx: It will search a protein database using your translated nucleotide query.

tBlastn: It will search a translated nucleotide database with your protein query.It will do the opposite of blastx.

tBlastx: It searches translated nucleotide databases with your translated nucleotide query.

Our protein here is collagen. If you put the above DNA sequence and blast it, the result shows sequence similarities with collagenIV of different species.

I think the reason to put sequence of collagen here is because it is a common protein. (in terms of databases it is profound)

Uniprot is a tool/program which provides the biological function of the proteins derived from the research literature. IThe Uniprot shows collagen has 5 disulphide bonds.

COL1A1 is its protein accession number.

The Protein Data Bank (PDB) is a database which provides the three-dimensional structural data of proteins and nucleic acids. The data is submitted by biologists and biochemists from around the world using X-ray crystallography, NMR spectroscopy or increasingly cryo-electron microscopy.

1BKV is the PDB number of collagen.

There are many macromolecular visualization tools like Rasmol, chime and MolMol. You can use these tools to check the structure, chemical bonds and polarity in collagen.

A ligand is a small molecule that is able to bind to a site in  proteins by weak interactions such as ionic bonds, Van der Waals interactions, hydrogen bonds and hydrophobic effects.

Drug designing, molecular docking are some applications of bioinformatics.