Question
In: Biology
ATGGTACTATCTCCTGAGTGCTGCAAGTTGTAACGGGCACCGCTGAGCCTGTTTCCCTTTGGAGCACTTC TTATCTAGAAGCAGTGTTTAGTTTCTTCCAAACTGGGCCACTTCGTCCACCTACTCTGTTCTGAGTAAGG AAACAGCCTCCAAGCATCAGCAGAGCCCAGATGAGCACGGGCCGCGGAGCCGCTTAGCAGTCTCCCGGGA CCCAGCTCCGGAGGAGCCGCAAGCATGCACCCTGGGTTG
Solutions
Expert Solution
(1) What does ORFfinder do?
Answer: Open Reading Frame finder are analytical tools having ability of finding all the open reading frames present in a particular sequence provided by using the standard/alternative genetic codes provided.
(2) What are ORFs?
Answer: Open reading frames are nucleotide sequences having a start codon (AUG) and a stop codon (UAA, UAG or UGA) as well and are able to translate into a protein sequence.
(3) How many open reading frames are there?
Answer:
1) ATG GTA CTA TCT CCT GAG TGC TGC AAG TTG TAA CGG GCA CCG CTG AGC CTG TTT CCC TTT GGA GCA CTT C
2) TTATCTAGAAGCAGTGTTTAGTTTCTTCCAAACTGGGCCACTTCGTCCACCTACTCTGTTCTGAGTAAGG
3) AAACAGCCTCCAAGCATCAGCAGAGCCCAGATGAGCACGGGCCGCGGAGCCGCTTAGCAGTCTCCCGGGA
4) CCCAGCTCCGGAGGAGCCGCAAGCATGCACCCTGGGTTGTGGCTGCTCCTGGTTACGTTGTGCCTGACCG
5) AGG AAC TGG CAG CAG CGG GAG AGA AGT CTT ATG GAA AGC CAT GTG GGG GCC AGG ACT GCA GTG GGA GCT G
6) TCAGTGTTTTCCTGAGAAAGGAGCGAGAGGACGACCTGGACCAATTGGAATTCAAGGCCCAACAGGTCCT
7) CAAGGATTCACTGGCTCTACTGGTTTATCGGGATTGAAAGGAGAAAGGGGTTTCCCAGGCCTTCTGGGAC
8) CTT ATG GAC CAA AAG GAG ATA AGG GTC CCA TGG GAG TTC CTG GCT TTC TTG GCA TCA ATG GGA TTC CGG G
9) CC ACC CTG GAC AAC CAG GCC CCA GAG GCC CAC CTG GTC TGG ATG GCT GTA ATG GAA CTC AAG GAG CTG TT
10) G GAT TTC CAG GCC CTG ATG GCT ATC CTG GGC TTC TCG GAC CAC CCG GGC TTC CTG GTC AGA AAG GAT CAA
11) AA GGT GAC CCT GTC CTT GCT CCA GGT AGT TTC AAA GGA ATG AAG GGG GAT CCT GG GCT GCC TGG ACT GGA
12) TGGAATCACTGGCCCACAAGGAGCACCCGGATTTCCTGGAGCTGTAGGACCTGCAGGACCACCAGGATTA
13) C AAG GTC CTC CAG GGC CTC CTG GTC CTC TTG GTC CTG ATG GGA ATA TGG GGC TAG GTT TTC AAG GAG AGA
14) AAG GAG TCA AGG GGG ATG TTG GCC TCC CTG GCC CAG CAG GAC CTC CAC CAT CTA CTG GAG AGC TGG AAT T
15) C ATG GGA TTC CCC AAA GGG AAG AAA GGA TCC AAG GGT GAA CCA GGG CCT AAG GGT TTT CCA GGC ATA AGT
16) GGCCCTCCAGGCTTCCCGGGCCTTGGAACTACTGGAGAAAAGGGAGAAAAGGGAGAAAAGGGAATCCCTG
17) GT TTG CCA GGA CCT AGG GGT CCC ATG GGT TCA GAA GGA GTC CAA GGC CCT CCA GGG CAA CAG GGC AAG AA
18) AG GGA CCC TGG GAT TTC CTG GGC TTA ATG GAT TCC AAG GAA TTG AGG GTC AAA AGG GTG ACA TTG GCC TG
19) C CAG GCC CAG ATG TTT TCA TCG ATA TAG ATG GTG CTG TGA TCT CAG GTA ATC CTG GAG ATC CTG GTG TAC
20) CTGGCCTCCCAGGCCTTAAAGGAGATGAAGGCATCCAAGGCCTACGTGGCCCTTCTGGTGTCCCTGGATT
21) GCCAGCATTATCAGGTGTCCCAGGAGCCCTAGGGCCTCAGGGATTTCCAGGGCTGAAGGGGGACCAAGGA
22) AACCCAGGCCGTACCACAATTGGAGCAGCTGGCCTCCCTGGCAGAGATGGTTTGCCAGGCCCACCAGGTC
23) CACCAGGCCCACCTAGTCCAGAATTTGAGACTGAAACTCTACACAACAAAGAGTCAGGGTTCCCTGGTCT
24) CCGAGGAGAACAAGGTCCAAAAGGAAACCTAGGCCTCAAAGGAATAAAAGGAGACTCAGGTTTCTGTGCT
25) TG TGA CGG TGG TGT TCC CAA CAC TGG ACC ACC CGG GGA ACC AGG CCC ACC TGG TCC ATG GGG TCT CAT AG
26) GCCTTCCAGGCCTTAAAGGAGCCAGAGGAGATCGAGGCTCTGGGGGTGCACAGGGCCCAGCAGGGGCTCC
27) AGGCTTAGTTGGGCCTCTGGGTCCTTCAGGACCCAAAGGAAAGAAGGGGGAACCAATTCTCAGTACAATC
28) CAAGGA ATG CCA GGA GAT CGG GGT GAT TCT GGC TCC CAG GGC TTC CGT GGT GTA ATA GGA GAA CCA GGC A
29) AGGACGGAGTACCAGGTTTACCAGGTCTGCCAGGCCTTCCGGGTG ATG GTG GAC AGG GCT TCC CAG GTG A
30) AAAGGGGTTACCTGGACTTCCTGGTGAAAAAGGCCATCCTGGTCCACCTGGCCTCCCAG GAA ATG GGT TA
31) CCAGGACTTCCTGGACCCCGTGGGCTTCCTGGAGATAAAGGCAAGG ATG GAT TAC CGG GAC AAC AAG GCC
32) TTCCCGGATCTAAGGGAATCACCCTGCCCTGTATTATTCCTGGGTCATACGGTCCATCAGGATTTCCAGG
33) CACTCCCGGATTCCCAGGCCCTAAAGGGTCTCGAGGCCTCCCTGGGACCCCAGGCCAGCCTGGGTCAAGT
34) GGAAGTAAAGGAGAGCCAGGGAGTCCAGGATTGGTTCATCTTCCTGAATTACCAGGATTTCCTGGACCTC
35) GTGGGGAGAAGGGCTTGCCTGGGTTTCCTGGGCTCCCTGGAAAAG ATG GCT TGC CTG GGA TGA TTG GCA G
36) TCCAGGCTTACCTGGTTCCAAGGGAGCCACTGGTGACATCTTTGGTGCTGAAA ATG GTG CTC CGG GGG AA
37) CAAGGCCTACAAGGATTAACAGGGCACAAAGGATTTCTTGGAGACTCTGGCCTTCCAGGACTCAAGGGTG
38) TGCACGGGAAGCCTGGCTTACTAGGCCCCAAAGGTGAGCGGGGCAGCCCTGGGACACCAGGACAGGTGGG
39) ACAGCCAGGCACCCCAGGATCTAGTGGTCCATATG GCA TCA AGG GCA AAT CTG GGC TCC CAG GAG CAC CA
40) GGCTTCCCAGGCATCTCAGGACATCCTGGAAAGAAAGGAACAAGAGGCAAGAAAGGTCCTCCTGGATCAA
41) TTGTAAAGAAAGGGCTGCCAGGGCTAAAAGGCCTTCCTGGAAATCCAGGCCTAGTAGGACTGAAAGGAAG
42) CCCAGGCTCTCCAGGGGTCGCTGGGTTGCCAGCCCTCTCTGGACCCAAGGGAGAGAAGGGGTCTGTTGGA
43) TTCGTAGGTTTTCCAGGAATACCAGGTCTGCCTGGTATTTCTGGAACAAGAGGATTAAAAGGAATTCCAG
44) GATCAACTGGAAAA ATG GGA CCA TCT GGA CGC GCT GGT ACT CCT GGT GAA AAG GGA GAC AGA GGC AAT CC
45) GGGGCCAGTCGGAATACCTAGTCCAAGACGTCCA ATG TCA AAC CTT TGG CTC AAA GGA GAC AAA GGC TCT
46) CAAGGCTCAGCCGGATCCA ATG GAT TTC CTG GGC CAA GAG GTG ACA AAG GAG AGG CTG GTC GAC CTG GAC
47) CACCAGGCCTACCTGGAGCTCCTGGCCTCCCAGGCATTATCAAAGGAGTTAGTGGAAAGCCAGGGCCCCC
48) TGGCTTC ATG GGA ATC CGG GGT TTA CCT GGC CTG AAG GGG TCC TCT GGG ATC ACA GGT TTC CCA GGA ATG
49) CCAGGAGAAAGTGGTTCACAAGGTATCAGAGGGTCGCCTGGACTCCCAGGAGCATCTGGTCTCCCAGGCC
50) TGAAAGGAGACAACGGCCAGACAGT TGA AAT TTC CGG TAG CCC AGG ACC CAA GGG ACA GCC TGG CGA ATC
51) TG GTT TTA AAG GCA CAA AAG GAA GAG ATG GAC TAA TAG GCA ATA TAG GCT TCC CTG GAA ACA AAG GTG AA
52) G ATG GAA AAG TTG GTG TTT CTG GAG ATG TTG GCC TTC CTG GAG CTC CAG GAT TTC CAG GAG TTG CCG GCA
53) TGAGAGGAGAACCAGGACTTCCAGGTTCTTCTGGTCACCAAGGGGCAATTGGGCCTCTAGGATCCCCCGG
54) ATTAATAGGACCCAAAGGCTTCCCTGGATTTCCTGGTTTACATGGACTGAATGGGCTTCCGGGCACCAAG
55) GGTACCC ATG GCA CTC CAG GAC CTA GTA TCA CCG GTG TGC CTG GGC CTG CTG GTC TCC CTG GAC CCA AAG
56) GAGAAAAAGGATATCCAGGAATTGGCATCGGAGCTCCAGGGAAGCCGGGCCTGAGAGGGCAAAAAGGTGA
57) TCGAGGTTTCCCAGGTCTCCAGGGCCCTGCTGGTCTCCCCGGTGCCCCAGGCATCTCCTTGCCCTCACTC
58) ATAGCAGGACAGCCTGGTGACCCCGGGCGACCAGGCCTAGATGGAGAACGAGGCCGCCCAGGCCCCGCTG
59) GACCCCCAGGTCCCCCTGGGCCATCCTCGAATCAAGGCGACACCGGAGACCCTGGCTTCCCTGGAATTCC
60) AGGTTTTTCTGGCCTCCCTGGAGAGCTAGGACTGAAAGGC ATG AGA GGT GAG CCT GGC TTC ATG GGG ACT
61) CCAGGCAAGGTTGGGCCACCTGGAGACCCAGGATTTCCCGGA ATG AAG GGG AAG GCA GGG GCA AGA GGC T
62) CTTCTGGCCTCCAAGGTGATCCTGGACAAACACCAACTGCAGAAGCTGTCCAGGTTCCTCCTGGACCCTT
63) GGGTCTACCAGGGATCG ATG GCA TCC CTG GCC TCA CTG GGG ACC CTG GGG CTC AAG GCC CTG TAG GCC TA
64) CAAGGCTCCAAAGGTTTACCTGGCATCCCCGGTAAAG ATG GCC CCA GTG GGC TCC CAG GCC CAC CTG GGG
65) CTCTTGGTGATCCTGGTCTGCCTGGACTGCAAGGCCCTCCAGGATTTGAAGGAGCTCCAGGGCAGCAAGG
66) CCCCTTCGGG ATG CCT GGA ATG CCT GGC CAG AGC ATG AGA GTG GGC TAC ACG TTG GTA AAG CAC AGC CAG
67) TCGGAACAGGTGCCCCCGTGTCCCATCGGG ATG AGC CAG CTG TGG GTG GGG TAC AGC TTA CTG TTT GTG G
68) AGGGGCAAGAGAAAGCCCACAACCAGGACCTGGGCTTTGCTGGCTCCTGTCTGCCCCGCTTCAGCACCAT
69) GCCCTTCATCTACTGCAACATCAACGAGGTGTGCCACT ATG CCA GGC GCA ATG ATA AAT CTT ACT GGC TC
70) TCCACTACCGCCCCTATCCCCATG ATG CCC GTC AGC CAG ACC CAG ATT CCC CAG TAC ATC AGC CGC TGC T
71) CTGTGTGTGAGGCACCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCGCAGTGCCCCCT
72) GGGCTGGCGCAGCCTCTGGATTGGGTACTCTTTCCTC ATG CAC ACT GCC GCT GGT GCC GAG GGT GGA GGC
73) CAGTCCCTGGTCTCACCTGGCTCCTGCCTAGAGGACTTTCGGGCCACTCCTTTCATCGA ATG CAG TGG TG
74) CCCGAGGCACCTGCCACTACTTTGCAAACAAGTACAGTTTCTGGTTGACCACAGTGGAGGAGAGGCAGCA
75) GTTTGGGGAGTTGCCTGTGTCTGAAACGCTGAAAGCTGGGCAGCTCCACACTCGAGTCAGTCGCTGCCAG
76) GTGTGT ATG AAA AGC CTG TAG GGT GGC ACC TGC CAC TCT GCC CCT TGC CCT CCC CTG CCC CTC ACA ACA G
77) TCACCTCACAAACCTGA ATG GTC TGA AGA AGG AAG GCC TGA GCC CCT TTG CCT GTC AAG TTG TAC ATT GG
78) AGTCTCATTTGGGCTAGACTACCGGACACTCGTCACCCCAGCCCTCGGGTCCATAGAG ATG AGC CCA CCC
79) TGCTGAGATCTGCTGTCCTGTTTCTGTCAAGCTGGTGCTACTGTTTGATTTGG ATG ATT GTG TGA CTA TT
80) C ATG GCT ACC TCA GAA AGA TTT GAT GGG CCA CAA CTG TCT TAG ACT GCT AGC TTT CTC CTT ACC GTC TTG
81) ATCGGAAAGCTCTTCCGAATCGCTAATCAGTCATTTCTTC ATG TAC AGA GGT CAG CAC ACA TTA TTT GGC
82) TTAAACCAGAACCCAGTGTTTCCACACTTAAATTCTCTAACCGAATATTCATG GAT GGC TCA AGT CTG CA
83) CAGAGCAAGTCCTCACTCTTCAAGGAGGCCCACTGTGTCTAGGCAGGCAAGAGAATTGAA ATG AGG TGC C
84) ACCCAGTAGCCCAGAGTGAGCTTTAGCTCTAGAATGAGCAAGACTGGGCCCCAC ATG GCT TAG AGA GGC T
85) TGAAGGCCAGCAGCTGGGTTGGGGGTGGTGGTCATTA ATG GCA TAT GGT CCT AGA CAA ACC ATC TCC TCC
86) TTGCCGGCTCCCCCTCCAGCCAGAGACAGAGG ATG TGG CCT GGT TCA AAG TAA AGC AGA GGA TGC AAC AA
87) ATG TGG CCA AGC TAT CAA AGG AAA TGA GAA TGA CAG CCT TTT TTC CTG GGC CAG AAG TAG AGG GGG TGG G
88) TGCGTAGG ATG TGT GAG TTT TGC TTT TGA CTC CAG GAA CAA AAA GGT AAA TCC CAC ATC CCA GTT TCT CA
89) GAAGTCCCTGTTTATTCCAATTGCCATCAGATGTGTGCA ATG TGG CAA ACT GAA GCT GCA CAG TGT TGG T
90) TTCCTTGTATTCTGAGG ATG TTA AAG ACT TTG TTA AAT GGT TAT CCA TT GCT CTT TCA CAG GTA GCC TA
91) TTAAACTATTTTAAT ATG TTT TTT TAA ACC TCA TAA AAA TCT AGC ACA CTC TTC TCT TGA GCA GTT AGC A
GACCACCG
ATG codon (green highlighted) (AUG in terms of RNA) is the start codon of the ORF from where the translation process starts. and TAA, TAG & TGA (voilet) are stop codons.
(4) Which reading frame do you think has a protein?
Frame:TGCGTAGG ATG TGT GAG TTT TGC TTT TGA CTC CAG GAA CAA AAA GGT AAA TCC CAC ATC CCA GTT TCT CA
Start:ATG
StopTGA
Nucleotide length: 21
Amino Acid length: 7
(5) If your protein is 25 amino acids long what is the nucleotide length?
Answer: 75 nucleotides, set of three nucleotides make a codon ( and each codon represents single amino acid (e.g. A U G for amiono acid Met). Therefore, 25 amino acids will have 25*3 = 75 nucleotides.
(6) What does BLAST stand for?
Answer: Basic Local Alignment Search Tool
(7) What does it do?
Answer: BLAST is a bioinformatics search tool helpful in identifying similarity between set of sequences. For example, if someone wish to find out similarity between different organisms for which the respective nucleotide sequences are given. Then, BLAST based on the local similarity between those sequnces can suggest evolutionaly relationships among given set of organisms. The main logic behind local similarity search is finding the similarity between the functional sites (say catalytic sites for enzymes that comprise of short regions). Such functional sites are conserved sequences. Thus, BLAST by finding out the local similarity produces meaningful & sensitive output than compairing the entire sequence length.
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