Results for “sequence-alignment”

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Alignment

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Embeds target and source image parquets, then mines nearest-neighbour source images for augmentation in VCN AOI workflows.

Analyze and automatically remediate MoonSpec artifact inconsistencies across spec.md, plan.md, tasks.md, and related design files. Use when the user asks to run `/moonspec.align`, identify uncertainty, weigh tradeoffs in project context, edit artifacts without asking follow-up questions, resolve coverage gaps, or align generated MoonSpec documents before implementation.

Use when you need to remove adapter sequences from high-throughput sequencing reads, trim low-quality bases, or filter reads by length. Supports single-end and paired-end FASTQ/FASTA input with error-tolerant adapter matching.

Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.

Curriculum Learning

LIMA: Less Is More for Alignment

当设定新目标或检视现有目标时，确保目标能通过高效的行为系统自动达成

Official GSAP skill for timelines — gsap.timeline(), position parameter, nesting, playback. Use when sequencing animations, choreographing keyframes, or when the user asks about animation sequencing, timelines, or animation order (in GSAP or when recommending a library that supports timelines).

Use when aligning low-divergence DNA sequence reads to a reference genome

CogVLM: Visual Expert for Pretrained Language Models

当寻求个人行动或项目在更宏大系统中的意义，或需要将日常工作与长远价值连接时

Visual Instruction Tuning

Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md. Identifying inconsistencies, duplications, ambiguities, and underspecified items.

Temporal interval algebra for reasoning about time relationships in planning and knowledge representation

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

Scaling Instruction-Finetuned Language Models

Mantis: Interleaved Multi-Image Instruction Tuning

Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

LLaVA-NeXT: Improved Reasoning, OCR, and World Knowledge

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Validate whether an OSS tool is worth building through staged namespace, existing-solution, and feasibility review

Use when aligning spliced RNA-seq reads to a reference genome, generating genome indices, or performing splice-aware alignment for transcriptome analysis.

SVIT: Scaling up Visual Instruction Tuning