{"id":18523214,"url":"https://github.com/iglee/smith-waterman","last_synced_at":"2025-09-06T19:34:29.208Z","repository":{"id":90698372,"uuid":"303930614","full_name":"iglee/smith-waterman","owner":"iglee","description":"Implementation of Smith-Waterman local alignment model- find closest local alignments in two given amino acid sequences. BLOSUM was used as the scoring matrix.","archived":false,"fork":false,"pushed_at":"2020-11-01T03:06:52.000Z","size":394,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-29T11:13:16.688Z","etag":null,"topics":["computational-biology","dynamic-programming","sequence-modeling","smith-waterman-alignment"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/iglee.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2020-10-14T07:03:37.000Z","updated_at":"2020-11-01T03:42:24.000Z","dependencies_parsed_at":null,"dependency_job_id":"6f61f592-3b37-4be2-8407-80a1dab5314b","html_url":"https://github.com/iglee/smith-waterman","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/iglee/smith-waterman","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iglee%2Fsmith-waterman","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iglee%2Fsmith-waterman/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iglee%2Fsmith-waterman/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iglee%2Fsmith-waterman/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/iglee","download_url":"https://codeload.github.com/iglee/smith-waterman/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iglee%2Fsmith-waterman/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273953790,"owners_count":25197368,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-06T02:00:13.247Z","response_time":2576,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["computational-biology","dynamic-programming","sequence-modeling","smith-waterman-alignment"],"created_at":"2024-11-06T17:34:37.242Z","updated_at":"2025-09-06T19:34:29.165Z","avatar_url":"https://github.com/iglee.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Implementation of Smith-Waterman local alignment\nThis is a repository for a CompBio assignment for CSEP527\ncourse assignment page: https://courses.cs.washington.edu/courses/csep527/20au/hw/hw2.html\nThe data was scraped from FASTA, and are located in `amino-acid-sequences` directory.\n\n\n# How to use\n\n- For string inputs, an example command usage is shown below\n```\npython src/smith_waterman.py --str-input -A \"AKA\" -B \"ak\" -o output/output.txt\n```\nNote: the input is not case sensitive.\n\n- For file inputs, an example command usage is shown below\n```\npython src/smith_waterman.py --file-input -af amino-acid-sequences/P15172.fasta -bf amino-acid-sequences/Q10574.fasta -p -o output/output.txt\n```\n**Caution: `-p` flag calculates p-value from Fisher Yates shuffles, so for fasta file inputs or long string sequences, it may take up to 20 minutes**\n\n- The shell script organizes the runs to generate HW2 report. In case you'd like to see more examples of the runs, please take a look at the shell script.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Figlee%2Fsmith-waterman","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Figlee%2Fsmith-waterman","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Figlee%2Fsmith-waterman/lists"}