(If several possible consensus strings exist, then you may return any one of them.). Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in FASTA format. the natural problem is to find an average-case strand to represent the most likely common Today, we’ll be looking at the Consensus and Profile problem. times that 'A' occurs in the $j$th position of one of the strings, $P_{2,j}$ represents Given a matrix A, we write Ai,j to, # indicate the value found at the intersection of row i and column j. def consensus (profile): result = [] keys = profile. Rosalind has 4 jobs listed on their profile. def consensus (profile): result = [] keys = profile. In this problem, we’ll be given a series of DNA strings, and our goal is to output a DNA string which represents the most likely common ancestor of all of the input strings (called the consensus string). TGTCCCATTTGTATTGGTTTTAGTCAATCCTTGCACGAGCAATTGAAACTGGGGCTCGAGGAGAACCACGGCTTGTTATAAGAATACGTCCCCTATATAAAGCCAAAGAGTGTCTGAACGACGAACGTAAGCTGTACTACAAACTCTTCATAAGCGGATGGATCATCCTGTCCCCCACCACGTGGCGTTCATCATGTACGGTTTAATTATAAACAATTGAGTGATATGAGCGTGCCTCATGTAATCTTTTCATTGTGGTAACAGCTTCCAAAGGCCCGCAATCTTTGATGTCTGATACCTGCATTAACCAATACGCGATCAGGCCCAACCAACATGCTTGTCCGGGAGAACATTGCTTACGTAGGTGGGTCCCTAGAAACTCTGGCAGCGTATTCAACATCGTAAGCCGGTTTACTGAGTCCTGAACGCGAATATTCTTGGCTAGCTCTTTCTTTGATAGGTTCTCCGGCAGTCTTCATACAACACCTGAGCGCACAGAGTTTGCTAACGCTCGCATATCTGCAGCGAGGGCATTCCTGACAAACGATACGGGGTATGCCCCCCGCGTACCACCCTACAGGAATGTCTTTCGTACGCGCTGCCACATTAACCCGGCTTCCATGTTACGGGAACGCGGTTCAGTTTGATAAGTAACGTTACTTCCGACAGAAGTCTCACGATCAAGAACTAATGGCGCGTTGCCAACGTGGCGTGATCTGCTAATGCCTGTTCTTTCAGATTTGCACTTCTCGGATATGTCGAATCTAGCATAGGAGAGACAAATGGCATTATCTGACAGTGGAATCCCCCTATTGAATCACTAGGCGCAAGAGTCTTCGTAATAGGGTCAATCCGCGAAGTAGCAAGGTGTTGACGTACGTGTTTCAAAGGACAGAGAAATGTCGGTCAGTTAGGCCACG, TCAAAGCAACCTAACAGCGATGCGGTTAAACGGCTGGTGACGGCTTCTGGTGCCGTACTGACACATAGGCTGCTTCCGTATACGAACCGAAGCCGAGGGTGATGCGCGCGCGCAGCGATCAACGGACCCCTGCCATCCGTCGCCCTTCAACTCAAGACCCAGCCAGTGTCCGTTCGGGAGCAGTCCAGCATCGGCCTATTAGACGTTGTTCTGTCTTTGCCACTGTCTGATCCGTTGTATGTGCATGGGCGGTTCCTATCATTAGGCGGTACGCAGATCAAAGGTGATGTGATGCTATCTGTAAGTAAGCGACTAAACCGTGGTAGTACGAATGGTATGGTCGCCTCCATCGAATCGGGAACGAAGGCGATTACTACTTAGCCCCAACCTTTTGGCACCCAGCACCGAAAGGCAACGAGATTTTAGAGATTGCTATCGTATAGGAAATTATGCTTGCCGCGTCACCCTAGTCAGTCTGCACAAATAACGAATCCATATGGGTAGGAAATATGGTAGAGGGATAAGGTTTCAACTCGAGACTGGGAATCAGAGCCGGCCTACAATTAGGCCTCGCCATGTAAGCACAGCGCAACAGCGGGGTTCCGGTGCGCTCCACCCCGGGCCGGCGTTACTCACATGTCGAGGTAGAGTAGCAGAACCACCTTCTGGTAACCGGCCCTTGGATAACAGTTGAAGTCGACAGTGAGGTTACTTGAGCCCAACAGGTGCGGGCTTCGGGGACTTCCCTTGTCTTCGGGCCAGCGGGCGACCCCGCCTGCTCCTATGAATAGGCCAATCCTGATGGCTCAAGATTTCCCGTCAAAATTCCCGCCCATCTCACCTTCCTGGAAGGTAGGGGTCTGGTTCTCTGGGCCTTGAGCCGCGTGAACGATTATTGCGGAGGGGGAGCGTGCGCAGTA, AGGTGTGCAGGGGATTCCATCTTGCAGTGGCCGACCTCCGAACGCGGAATTGGAGCTCGCAAATGCTTGTGGGAGGATTTCGTAAGTGGGAACTTCTGTGCGGGATCCACCTGGTAGGGGTATGACCCGTCTGCTATTATTTAACACGCTACTATATGCCTAGGGGGCCTCGATTTCAAGCATTTCAGGTCATTTTCATCTGTGATCTTCCATCCGAATACCTCCACGTCTCTAGATCGTGGCAATGTATGGGCCGTTCATACCAACCCTGTGCCAGTCCTAACAATACATTTACGAGTCTGGCACGTCCTTGTAATGGTCCTGCTTTCATGGCTGTCGCGGCCTGGTAATTGTCCGTCAAGCTATTAACGGTCGCACGAAAGGAGCGCATGTGCTCCATGATAGGGTCAGATAACCCACCTTTGACATTCTGTATCTGACTTTGACTCCAACTCAAGGCCGTTATTTCCGGGGTTGAAACAGTAACACGGATATCAGATGCTGAGCCAGCCCTGCCTACGATACAGCACAGCCAGCTCCCCAGTCCTGACGTAAGATTCCAGGGGATCGCACAGCCAATGCTCACCGCATCACTAGACGTGGCATTCGCTCATCAGGAGTATATCCGCACTTTGCTAACCCTCCGTGCTGCCCTCATACTTTCGTCATAATTCGATCTTCATCCGGTTTTATTTCCAGTGGACGAAAGATGCTGCTTGCGCCGTACCTTAAACATTGTGCCTCCAGCGAAGCAGGATGGTCTGCTGAGTCCACTCCACGGGCAGAGAAGCGTGACGTACTTGGAGTTCCAATTCAACGCTAATTTGTGGCGTGGAGTCCGCGCGTCCGGGGAACCGAACAATTTTCCCGATCAACGGAGATGCTCATAAATTTATAGTTTGATCTAAAGGTTGTCAAAA, GGGAGCCTAAGGACACCCTATGCGTTAGTTGCAGTGGTTCGACGCTAGAAAGGCTTTTCCAGATTAAGACTCCATGAACTTCTCGAATCCGTGGGGCTCCCGTCAACTGAAGAGATACGCGCTCCTGCGCGCAGTACATTGACCCCATAGTGCTCGTGGTCCGCGGTCAATCGACGTCTGGCTGATTGGAACGCGTAGTGTCAGGGGTACGCATGCCGACTCAGCGCTGCAACCGTAGCGCTTCCAAGGTAACCGTAAGTTTGTGGCCAAACGCACGTTTTATTCTCGTAATGGTCGTGCGACTCGATTGAATCACTAACCTTATGGGCTGCAAATGTCCAATTAACTCGCTCGCGATGGAAAGACCGAGAACCCTTCTTCAATGGTGAGTTGCGCGCAGCATAAGAAAAAGATGTCAGTCCGGTCTGTGCGATTTAGGGGATCTTCCCTGGGCAGTGTGTGTCGCATAGGGCTCGGCGTAGGATATTGTTGATAGTAATTCGGAAACGGGCGCTCGCTCAATACACGCTGAGATGAAGACTACAGAAACCTTGCGCGCCACGACTAAGGCTGGGGGTCCCAAACAGCTCGATGGAGCTTAGTCTCTGCCCGACTGTATTGACACGTTGTGCGTTGATTTGTAGGGGAGACGGTTATAAGCGATGCTGTAGCGGTACCGCCACACAGAGTAGCCACTATGCGTTTACGGATTATATACGAGGCAAGATCATCACTGTTTGTGACCGATTGCGGCTCCTCAGCCAGCCAATTGTTCTTCTAGCAAGGAGCATGGTCTGGCGGAATGGCGGGCTCAAAGGTTGGCCAATCAACTCATGTGAGCGTAATGATGAAGTTTCCACCAACACACACATTCTAACGCAAAACGATGCACACTTAGGAGCACGGATACACTTGGCATG, CCAATGATGGTCCCCCTCGCAGCGAGGAGGTAGATATCCGGCACCTTAGGGTAAGGCGGGCCAGAGAGTTTCAGCTCACTGATGTGAGGAGTGAGTCAGAGCAATATCGGCTCATCATTCAAGGTCCAACATGTGCATGTGTTAGTATCATTTCTTCTGGGGATCTCAATCACGTCGCACATCTCGACGTCACGTTTTTACGCATGCAGAAAGGTAGTCCATAAAACTCAGCAACTCATTTAATGTGAAGGCACCGTACTCTTGAACGGGGTATAGAGATTGGAGGACCGCCGGGTGCGTTAGAACTATATAGGCACAAGGATGCGGCTTTATATCCTAAAGCCGGCGCGGTGAAGCTTATACAGCACCTGCATTGCTAGCCACATGAGTCGATTGCAAACCAAGGTTACGCAGCCGCGCAAAGTCATGCCACGTGAGCGGTAAAGGCCCCGCACACCCACATCCGATTGGGGAGCGTCTGATATCTGTTCCCTACTCCTGCCCGTCTCGTAGTGTGGTCCACTAATACCCCATAATGACTAGGGATACTATGTCGTATATCACTTATCCTAACCCATCTGGATACGACCTCCGAAACGATCCGGTTACCACGATATTAGGAAAGAGCTGTAGTGTCCCGTAAGTCAGAATTCCTGCATGTTTGAGTTCCAGATTTGTCATCGGCAATGCTACTGGAGAACGGCCAAGATACATCGGTAGCAAACTGCAGTACCAGGAGCGGCACGACGAGGGTAATTATCTGCTGTTTGTCATGTCGGCTCTCGACGAGCCTCACTCCAGTCGCCAGACCAACGTGGATAGGCGCCACGGTGAAGCCATAGAAACCATACGGATTTGAACCCTAGGCAATATCTTCAAATTTATGGAACACTGCCTAAGATTCTGTTATTTGATCGGCA, ACGTAAGTACGATAAGATTGCTAACATGGATTGTTAAATCTCTCTCGGACGGTATGTAATACACAGTCGTAGATCGTTCTACTCCCCATCGCCTCTGCCTCTGAATACCACACTCAATCGCGGACCCTATATTAAAAAAATGTCTACCAGCGTACGTCACATTCGGTCTCTCTGTAATGAAGGGGCTTGCTTGCAAACCGTCGGCGGCGCCGGGAAGATCTGAACATACCGACTAGTCATTACTACGGGCCCTGCGCGCATTTAATGCTGATTGATAAACTATGTTATGGGTGATGATCTCGCGGAGGGGGTTATCCGCCTAGCTCCTAAGTAATAGGCACGCCCGTTTTGAAGCTTCGGGCCGCTTTCAGTCTGGCCACCTTGAAGAGACAATTGAGTTGGAGGAGTATTATGAACCTCTACCACGCAACCTCCGTTGTGTTTTGGAGACCTGGCCGCACTGCGTTACGGGGGCAAAAGTATGCTGAGTCATGGAGTCTCCCACACAGGCTTCACCTTAACCCTAGCCAAGTGGAGCAATTTTCCGGCGGGCTAATTGTTCTGGTGGTGCTACCAGGACGTATACATTGACTTAGTTGATAACTTAATCGCTTTCTCCTTCCGTGTATGGCGCCCAGTGTGCGTGCCGGAGTCACAGCCAACTCAAACAAGCTTTTCCTGGTCATGCGTCAACGCGTCTATTACACGCTCCATTTTCTGGGTGCCACCAGTATCGCGTGGTTTAAACCCATGTATGGTTGCTGCCGAGCTGCATTAGACCTTCGATGCCGCTAATGTGAGCTCGGTCAGTTAACCTACCCAAGTCTCACTCGGAAGTATATTACTGACCAGGTCAGCCGGAAGAAGAACTAGCTGTGCCAAAGGAGGCTCGCTTGGGCTGGAACCATAGCCCCGTATCT, CAATCATGGATCGCTTCGCTGGGTGTGCGCAGCGAGTCTTCGACTGAGAGTGGTGGTTCCTTCAACGTTTTTTACTTTCCGCATCTATCTGGGTTCTCTTTAGTTGGCGTTCGAGGGTAATGTCGATTAGACGTCCAGCTCTTCCATAATGTTGGCGCACTCCGTGTGCTTATCATCAAAGTCCAAGTTTTCATGTATAAAAAAGATGTGCCGCGTGTCTCGCACGTATCTCCACTTTTAACTTTTGGCTTAAACGTTGGGATACTCGCTCAGTCCCTCCGACTCCTGTCAATTGAAGGCCTAAGGGGTCCATAATCTGCTTGTGTCCCCTTAGGGTAAAATTGATCTTAGGCCTGAATGCTGAGTCATCAAAACACGTTCGGACTACATGGATCCAAGAAATAAGGCGCATCTCTACGACTATTGACTCCACTCACGCCCCGCTCAAAGCAGCAACACTTTCTGCACGTATCTTCTGCTGAAGTATGTACCACCGCGAGAAAAGGGAGACGGTCTTAACTGTTCCACCTAGACATTACAAAGAATCTAGGCCCCGTCACTTACATAGAACTACCTACGTCGAGGGGCGGTAATGCCATCACTGGTGAAGCATAGGCATGTACTCTAGCCCGCTTTATTTGCCAATGAGGGTAGACACAAGGGATGGCGTGTTCGTCCCATGAACTTTGTTCTTTCCACTTAAAAATTAAGATACAGGGCGCCGTGTTAGTCCTTATGCGCTATCCCTTGTCACCCACTTGTGGTGCCCACAATCTGCGGGGGTGACCGTGATGCTCTTGCCTTAAGCTTCACCAATGGAATTAGCGGAATGGGAACCTAGTGTGTTATCTCACGAGTAAGACTTTTTGCAACAGATAATACTTCGAAGAATTTACAAACCCGATGGGCCTGCTGCCGTC, ACATTGACTCACTTTTCGCGGAGAGACATTGGTTCCGTAATCTGTATATGTGGGAATAGCAACATTCTAACTTTGTGGCCATTACGCTGCCCTAGCCCTAGCGGCGTATGCTCAGACTCGTGGGTTAAGAACTTTTGTGCGCAAGGATATGCACGGACGTGCATTTCGCACCCCCCAACATGTATAGGTTATCGCAATTTCCCAGGCAGCTGGAATGCAGACTGCTCCACGTATGGGCACATGGCCGCGCTACCGAGCCTTTGACATTTATTTGCGCCTTCCCCCGTCCCTACGGACGATCAGTAAGACCGTAGCGAATCTCCCTGTACGCCACTATCAAAGGCCTAAGGAGGCATCACCTCCACAAGCCACGCAAGGTTAACGATAGTTTTAACTAACTATTTGACTTGTAGTTCCAGTCTGTCCTGGGAGGCCTAGTAGCTGTCTCACAAGGTTGCACATAGTTGTGTCCTTGGGGAGACCTGAGCTGGTATTACAGTTCGGCTGGGTCCACAGGACTATTGCGTTGTGGATTACGGCCGTTACGCCAAATAACGCCATACCGGCCATCATGTAAGCTATCGCCGTTCCTAGAGTCACCTTATTCTACCGGAGTTATCCGATCTAACCACGGACGAACCGGGCACTCTCTTGAACTTGTGAGAAATCGATAGTACAAGCGGCTCATTCTATCCTCGAGTGTTCAGCTATACTGTCTGCGATGGATGATTGCGCTTTTATCCATAAGCTTCGTAGATCAGGTAAGATTAGCCGCCCTGGCTTCGACCGTAAGAGAAATGCTTTAAGTGTGTTGCGAGTCGAGATCCACAGCAATCGGGTATACATGTCGAGGACATTGTACTTACCTTATACCCAGGTCACGCCCCCTGAAGATACATGCGCTTGGACACAATCGTAAT, TACCCCGTCTTTCACAGGGCTTCCAACCTCAACAGGCGCGGCTCTTGGTAAATGGGATAATGTGCGATGGGCGTAGCGTCGAATAGCCGGCTAGTAAAGGGCAAAAGCATCTGGGCGAGCTTCGGTCGCTGCGAGGTCTCTGCAGCGCGTATTTGTATAAGCCTCCCACCGGCCCAGAATAGCCATATGGATGTGGCCGGGAAATGTAGTGTAAGCAGTGATATGCCTCCAATCCCTGCCCAAGGACTATCCTGTACCATTTTATCAAGCCAAACTATCCAGTAGGACAAGGCCCCATACGTAGCGAATACGTATCGAAGAGTTATCGCAAGCCCCATGTAAGATGACCATAGCAATGTGTTTCTTACCTGCCTTTGATTACAGGTACTCCCGATAAGAGTGAGCGAAACGGGATTGGCTAGACGTCAGCCTGGTACCGCGCCGCAAGCCTCAAGCTCGATGAGGTTAGAAGACGTACCTGTAGTCGATCGAACTCACTGTGGCCTGCCGAGTGACAATCAGCAAGAATCGCGAGATGGACGTTAGCCGTCACTAAAAGCGCTTGAAGCAGACGGGTCTCTCGTTCACACCATCGCCGATAACAATCAACCTGAGGAGTGCAGCATCGAGTATCTCCTGCGGTCGTGTGCCACTAGTTATAGAAGATTTACGGGTTTTTAGATATCCAGGCTATATGGCTTTGTAGGTTAGGTTGTATAGGGTAGATAATGAACTCGCGTGACGATAAAATTCACCCGCTTTACCGTGGCAATTTAGGTTCGTATTATTCGTTCCAATGTAGTCCCGCGCGCGCCCGTCAGTCGAAAAGCTTGCACGTTAGTACCACAGAATCCCCAACGTGAGAGCGTATTTAATCTATGAGCCGCTCAAGGACTCTTGGGTTTCGTGTGACGATGTAT, TTTCTCGGTCACCTCGTCTATGTCGATATGGACTACCTTGAATATTCGGATTGAGACATCAGCCCGGTACATGGCCCAGTTGGGGTGCCAAGTCTAACTCGAGTTTTGTCGACAGCCAGACATTAAATAGAGCCCGTGGTCTGCCGCAATCCTTCCTTGGACAGCGCAGGCCTCCTTCACTATCGTTGGTCAGAAAATACCAAAGTAGCCCGCTACCATAGAACCCCCAGCCGGGCCAACCGTCCTTAGTCGAGTAGCATGGGAGCATATCGTTCGGGACGCTAGACCGAGTACAGCACCCCTCCTGACCGGCTCCTCGAACCTTCGGTGACCCTCGAATGGTTTTTCGCATCCTTGATGTTCTACATCCGCCGATTTCTAACGTGCTACAATGGTCCAAAGCTGCACCTCCGCCCCTAGCGGTAACGGGTGTGTAAGAGGTAGAAACGAATAGCATTGGTCCCTCCACATCAGACTATCTCAAGACAAGTGTGCAGATGGCAACCAAGCAGTTATTTAACGCAAGCCCGGCCGTGAACGAAATCCCCCTGCGGCATTTTTAACTGTCAGTCTTTATAGGTGCTATGACGAGGTATGTTGATGTGCGGAATCCCCAAGGAGCCAGGGTGGAGCTCAATTACACAAAGGAGAGTTCAGCTATGACGGATGCCTATATATAGACGCAATTCGATAGAAGTTCTAAACGCGCTGTAGGGTGTTCATGTGACACGTAACTTCGACAACATTGACGGCTACACATCCCTCTTTGTTGCTAATACGCCCGTTAATATACCCACGCCAGTATTCGAACTCAGCTGTGGGGAGTTTTGTCCATTAAAATCCTTCCGATCTTTGCACGGTCGTACCCCAGAGCTTGACATTTTCATATGACGGGGAGCATCACGCGTAGGAGGATCCAG, # A matrix is a rectangular table of values divided into rows and columns. View Rosalind Estes’ profile on LinkedIn, the world’s largest professional community. It appears that your browser has JavaScript disabled. Model ( cons.rb ): keys for i in range (len (profile [keys [0]])): max_v = 0: max_k = None: for k in keys: v = profile [k][i] if v > max_v: max_v = v: max_k = k: result. append (max_k) return ''. Return: A consensus string and profile matrix for the collection. Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in FASTA format. profile matrix is a $4 \times n$ matrix $P$ in which $P_{1,j}$ represents the number of Quality of life and patient reported outcome measures (PROMs) are important secondary endpoints and incorporated in most contemporary clinical trials.… Problems: 285 (total), … # Return: A consensus string and profile matrix for the collection. Skylign accepts sequence alignments in any format accepted by HMMER (this includes Stockholm and aligned fasta format). ... For the third part the program needed to evaluate the profile matrix and create the consensus sequence (any one of them would suffice in the case that there were more than one). Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models. Rosalind in F# – Consensus and Profile Today, we’ll be looking at the Consensus and Profile problem. $m$ rows and $n$ columns. Rosalind - Consensus and Profile. Problem: Please find the problem here. corresponds to the symbol having the maximum value in the $j$-th column of the profile matrix. at each position; the $j$th symbol of $c$ therefore # Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp). In this problem, we’ll take a series of DNA strings and find the most likely common ancestor of all of them by calculating the consensus string. # choose to think of A as a collection of m arrays, each of length n. # Say that we have a collection of DNA strings, all having the same length n. # Their profile matrix is a 4×n matrix P in which P1,j represents the number of, # times that 'A' occurs in the jth position of one of the strings, P2,j, # represents the number of times that C occurs in the jth position, and so on, # A consensus string c is a string of length n formed from our collection by, # taking the most common symbol at each position; the jth symbol of c therefore, # corresponds to the symbol having the maximum value in the j-th column of the. found at the intersection of row $i$ and column $j$. Rosalind in F# – Consensus and Profile. Given a matrix $A$, we write $A_{i, j}$ to indicate the value Bioinformatics Algorithms. append (max_k) return ''. (If several possible consensus strings exist, then you may return any one of them.) A matrix is a rectangular table of values divided into rows and columns. In this problem, we’ll take a series of DNA strings and find the most likely common ancestor of all of them by calculating the consensus string. Return: A consensus string and profile matrix for the collection. Download Code. Sample input. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.