{"id":24394401,"url":"https://github.com/bibymaths/perl_snippets","last_synced_at":"2026-04-14T18:33:59.033Z","repository":{"id":273130415,"uuid":"918788731","full_name":"bibymaths/perl_snippets","owner":"bibymaths","description":"A collection of Perl scripts for solving bioinformatics problems and algorithmic challenges, including sequence analysis, alignment, and DNA assembly.","archived":false,"fork":false,"pushed_at":"2025-01-21T16:41:04.000Z","size":28,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-05T12:43:09.425Z","etag":null,"topics":["alignment","amino-acids","assembly","bioinofrmatics","dna-sequences","edit-distance","fibonacci","hamming-distance","lcs","motif","perl"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bibymaths.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-01-18T21:19:05.000Z","updated_at":"2025-01-21T16:41:07.000Z","dependencies_parsed_at":"2025-06-27T22:34:37.292Z","dependency_job_id":"7b6c22a8-5a6f-4fb4-90ce-00ed59906686","html_url":"https://github.com/bibymaths/perl_snippets","commit_stats":null,"previous_names":["bibymaths/perl_snippets"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bibymaths/perl_snippets","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fperl_snippets","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fperl_snippets/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fperl_snippets/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fperl_snippets/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bibymaths","download_url":"https://codeload.github.com/bibymaths/perl_snippets/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fperl_snippets/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31810737,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-14T18:05:02.291Z","status":"ssl_error","status_checked_at":"2026-04-14T18:05:01.765Z","response_time":153,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alignment","amino-acids","assembly","bioinofrmatics","dna-sequences","edit-distance","fibonacci","hamming-distance","lcs","motif","perl"],"created_at":"2025-01-19T19:24:14.317Z","updated_at":"2026-04-14T18:33:59.002Z","avatar_url":"https://github.com/bibymaths.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bioinformatics and Algorithmic Problem Solvers\n\nThis repository contains a collection of scripts designed to solve common problems in bioinformatics and algorithmic puzzles. These Perl scripts can be utilized for DNA sequence analysis, optimization problems, and mathematical challenges.\n\n## Table of Contents\n\n1. [Scripts Overview](#scripts-overview)\n2. [Requirements](#requirements)\n3. [Usage](#usage)\n4. [Scripts Description](#scripts-description)\n5. [License](#license)\n\n---\n\n## Scripts Overview\n\n| Script Name                      | Description                                  |\n|----------------------------------|----------------------------------------------|\n| `fibonacci_series_calculator.pl` | Generates Fibonacci series numbers.          |\n| `tower_of_hanoi_solver.pl`       | Solves the Tower of Hanoi puzzle.            |\n| `dna_distinct_substrings.pl`     | Finds all distinct substrings in DNA data.   |\n| `hamming_distance_calculator.pl` | Calculates the Hamming distance between sequences. |\n| `amino_acid_to_dna_converter.pl` | Converts amino acid sequences to DNA codons. |\n| `global_alignment_wunsch.pl`     | Performs global sequence alignment using the Needleman-Wunsch algorithm. |\n| `local_alignment_smith.pl`       | Performs local sequence alignment using the Smith-Waterman algorithm. |\n| `edit_distance_calculator.pl`    | Computes edit distance between strings.      |\n| `motif_identification_profile.pl`| Identifies motifs using profile matrices.    |\n| `longest_common_subsequence.pl`  | Finds the longest common subsequence between strings. |\n| `dna_fragment_assembly.pl`       | Assembles DNA fragments into sequences.      | \n| `euclid_pdb.pl`       | Calculate and print the distances between atoms.      | \n| `dna_mutation.pl`       | Randomized mutation of genomic sequences.      |\n\n---\n\n## Requirements\n\n- **Perl**: Ensure you have Perl installed on your system. Most Unix-based systems come with Perl pre-installed.\n\n## Usage\n\n1. Clone this repository:\n   ```bash\n   git clone https://github.com/your-username/bioinformatics-scripts.git\n   cd bioinformatics-scripts\n   ```\n\n2. Run the scripts using Perl:\n   ```bash\n   perl script_name.pl\n   ```\n\n3. For scripts requiring input, provide the necessary arguments or input files as specified in the script comments.\n\n---\n\n## Scripts Description\n\n### `fibonacci_series_calculator.pl`\nGenerates Fibonacci numbers up to a specified limit. Useful for sequence-based problems.\n\n### `tower_of_hanoi_solver.pl`\nSolves the Tower of Hanoi puzzle and outputs the steps required to move all disks from one peg to another.\n\n### `dna_distinct_substrings.pl`\nAnalyzes a given DNA sequence and outputs all distinct substrings, aiding in sequence pattern recognition.\n\n### `hamming_distance_calculator.pl`\nCalculates the Hamming distance between two DNA or RNA sequences, measuring the number of differing nucleotides.\n\n### `amino_acid_to_dna_converter.pl`\nConverts amino acid sequences back into possible DNA codons, useful for reverse translation.\n\n### `global_alignment_wunsch.pl`\nImplements the Needleman-Wunsch algorithm for aligning two sequences globally.\n\n### `local_alignment_smith.pl`\nImplements the Smith-Waterman algorithm for local alignment of sequences.\n\n### `edit_distance_calculator.pl`\nComputes the minimum number of edits required to transform one string into another.\n\n### `motif_identification_profile.pl`\nUses profile matrices to identify motifs in DNA sequences.\n\n### `longest_common_subsequence.pl`\nFinds the longest subsequence common to two given sequences.\n\n### `dna_fragment_assembly.pl`\nReconstructs DNA sequences from smaller fragments using sequence overlaps. \n\n### `euclid_pdb.pl`\nCalculate and print the distances between atoms with the maximum distance for each atom in the first set relative to atoms in the second set. \n\n### `dna_mutation.pl`\nReads a DNA sequence from a file, mutates it at random positions to create successive variations, and prints the original sequence, the first mutation, and 10 successive mutated sequences.\n\n---\n\n## License\n\nThis repository is licensed under the MIT License. See the `LICENSE` file for details.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fperl_snippets","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbibymaths%2Fperl_snippets","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fperl_snippets/lists"}