How does it handle random access in large genomes?

It utilizes the faidx index format via pysam.FastaFile to fetch specific genomic regions efficiently without loading the entire file into memory.

What file formats does the Sequence I/O skill support?

It natively supports FASTA, GenBank, and FASTQ formats for reading, writing, and conversion.

How does it handle 0-based vs 1-based coordinate systems?

The skill follows Biopython's 0-based Python-style slicing for sequence objects and provides clear guidance on pysam's dual-system handling for numeric vs string region fetching.

Does this skill provide tools for sequence statistics?

Yes, it includes utilities for calculating GC fraction, molecular weight, melting temperatures, and codon usage analysis.

Can I use this skill for large NGS data like SAM or BAM files?

No, for NGS alignment files like SAM, BAM, or VCF, you should use the pysam library directly as this skill focus on sequence-level I/O.

Biological Sequence I/O

Name: Biological Sequence I/O
Author: dakesan

bydakesan

데이터 과학 및 ML

Reads, writes, and manipulates biological sequence data formats like FASTA, FASTQ, and GenBank.

소개

This skill provides a comprehensive toolkit for bioinformatics workflows, enabling Claude to parse and convert various sequence file formats, perform sequence manipulations like translation and reverse complementation, and efficiently access large genomic files via indexed random access. It integrates industry-standard libraries like Biopython and pysam to handle everything from simple sequence statistics to complex genomic data extraction, ensuring high-performance processing of biological data while managing coordinate system nuances.

주요 기능

0 GitHub stars
Multi-format support for FASTA, GenBank, and FASTQ files
Indexed random access for large FASTA files using faidx and pysam
Automated calculation of GC content, molecular weight, and melting temperatures
Built-in sequence operations including complement, reverse complement, and translation
Streamlined format conversion between biological sequence standards

사용 사례

Converting GenBank files to FASTA for downstream computational analysis
Analyzing DNA sequence properties like GC content and Tm for primer design
Extracting specific genomic regions from large reference genomes using coordinates

소개

주요 기능

0 GitHub stars
Multi-format support for FASTA, GenBank, and FASTQ files
Indexed random access for large FASTA files using faidx and pysam
Automated calculation of GC content, molecular weight, and melting temperatures
Built-in sequence operations including complement, reverse complement, and translation
Streamlined format conversion between biological sequence standards

사용 사례

Converting GenBank files to FASTA for downstream computational analysis
Analyzing DNA sequence properties like GC content and Tm for primer design
Extracting specific genomic regions from large reference genomes using coordinates