Biopython · GPTomics/bioSkills

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO.

GPTomics/bioSkills

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.

GPTomics/bioSkills

Parse and analyze multiple sequence alignments using Biopython.

GPTomics/bioSkills

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner.

GPTomics/bioSkills

Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic.

GPTomics/bioSkills

Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW.

GPTomics/bioSkills

Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary).

GPTomics/bioSkills

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).

GPTomics/bioSkills

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee.

GPTomics/bioSkills

Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx.

GPTomics/bioSkills

Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences.

GPTomics/bioSkills

Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools.

GPTomics/bioSkills

Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64…

GPTomics/bioSkills

Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM.

GPTomics/bioSkills

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO.

GPTomics/bioSkills

Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring.

GPTomics/bioSkills

Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized.

GPTomics/bioSkills

Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio.Phylo plus R ape/phangorn/FastME.

GPTomics/bioSkills

Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (treeio, DendroPy) when metadata matters.

GPTomics/bioSkills

Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rather than a display choice.

GPTomics/bioSkills

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access.

GPTomics/bioSkills

Select restriction enzymes for cloning or diagnostics using Biopython Bio.Restriction.

GPTomics/bioSkills

Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction.

GPTomics/bioSkills

Design and validate Type IIS scarless DNA assembly (Golden Gate, MoClo) using Biopython Bio.Restriction.

GPTomics/bioSkills

Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction.

GPTomics/bioSkills

Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction.

GPTomics/bioSkills

Generate reverse complements and complements of DNA/RNA sequences using Biopython, including IUPAC ambiguity codes, gapped alignments, and minus-strand features.

GPTomics/bioSkills

Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython.

GPTomics/bioSkills

Calculate nucleotide and protein sequence properties (GC content, GC skew, molecular weight, melting temperature, isoelectric point, instability, hydropathy) with Biopython.

GPTomics/bioSkills

Slice, extract, and concatenate biological sequences and annotated records using Biopython.

GPTomics/bioSkills

Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity handling, summary reports) using Biopython.

GPTomics/bioSkills

Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD…

GPTomics/bioSkills

Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB.

GPTomics/bioSkills

Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities.

GPTomics/bioSkills

Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding.

GPTomics/bioSkills

Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes…

GPTomics/bioSkills