Rosalind Challenges

Bioinformatics algorithms written in python

My profile: benigmatic

Bioinformatics Textbook track

Summary

• Problem ba1a: Compute the Number of Times a Pattern Appears in a Text. Code

• Problem ba1b: Find the most Frequent Words in a String. Code

• Problem ba1c: Find the Reverse Complement of a String. Code

• Problem ba1d: Find All Occurrences of a Pattern in a String. Code

• Problem ba1e Find Patterns Forming Clumps in a String. Code

• Problem ba1f Find a Position in a genome Minimizing the Skew. Code

• Problem ba1g Compute the Hamming Distance Between Two Strings. Code

• Problem ba1h Find All Approximate Occurrences of a Pattern in a String. Code

• Problem ba1i Find the Most Frequent Words with Mismatches in a String. Code

• Problem ba1j Find Frequent Words with Mismatches and Reverse Complements. Code

• Problem ba1k Generate the Frequency Array of a String. Code

• Problem ba1l Implement PatternToNumber. Code

• Problem ba1m Implement NumberToPattern. Code

• Problem ba1n Generate the d-Neighborhood of a String. Code

• Problem ba2a ImplementMotif Enumeration Code

• Problem ba2b Find a Median String Code

• Problem ba2c Find a Profile-most Probable k-mer in a String Code

• Problem ba2d Greedy Motif Search Code

• Problem ba2f RandomizedMotifSearch Code

• Problem ba2g Implement GibbsSampler Code

• Problem ba2h Implement DistanceBetweenPatternAndStrings Code

• Problem ba3a Generate the k-mer Composition of a String Code

• Problem ba3b Reconstruct a String From its Genome Path Code

• Problem ba3c Reconstruct a String From its Genome Path Code

• Problem ba3d Construct the De Bruijn Graph of a String Code

• Problem ba3e Construct the De Bruijn Graph of a Collection of k-mers Code

• Problem ba3h Construct the Overlap Graph of a Collection of k-mers Code

• Problem ba3i Find a k-Universal Circular String Code

• Problem ba4a Translate an RNA String into an Amino Acid String Code

• Problem ba4b Find Substrings of a Genome Encoding a Given Amino Acid String Code

• Problem ba4c Generate the Theoretical Spectrum of a Cyclic Peptide Code

• Problem ba4d Compute the Number of Peptides of Given Total Mass Code

• Problem ba4f Compute the Score of a Cyclic Peptide Against a Spectrum Code

• Problem ba4h Generate the Convolution of a Spectrum Code

• Problem ba4j Generate the Theoretical Spectrum of a Linear Peptide Code

• Problem ba4k Compute the Score of a Linear Peptide Code

• Problem ba4l Trim a Peptide Leaderboard Code

• Problem ba5a Find the Minimum Number of Coins Needed to Make Change Code

• Problem ba5b Length of a Longest Path in the Manhattan Tourist Problem Code

• Problem ba5f Find a Highest-Scoring Local Alignment of Two Strings Code

• Problem ba9b Implement TrieMatching Code

• Problem ba10a Probability of a Hidden Path Problem. Code

Bioinformatics Armory [COMPLETED]

Summary

Problems not listed were completed with software provided

• Problem 1 Introduction to the Bioinformatics Armory Code
• Problem 2 GenBank Introduction Code
• Problem 4 Suboptimal Local Alignment Code
• Problem 6 FASTQ format introduction Code
• Problem 7 Read Quality Distribution Code
• Problem 8 Base Quality Distribution Code
• Problem 9 Base Filtration by Quality Code
• Problem 11 Protein Translation Code
• Problem 12 Complementing a Strand of DNA Code
• Problem 13 Finding Genes with ORFs Code