CROSSTCR Utilities

Tools Hub

A focused workspace for CROSSTCR batch lookup, sequence-level comparison, pMHC context review, and curated TCR cross-reactivity prediction resources organized from the supplemental material.

Guided modules

CROSSTCR utility workspaces

Curated tools

Prediction and analysis resources

Displayed

Matching current filters

Publication span

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Based on curated tool records

Tool Directory 6 modules

Interpretation notes

These utilities support exploratory analysis. Sequence similarity, tool annotations, and prediction outputs should be interpreted with experimental evidence and source context.

Priority 2

Batch Query / Batch Annotation

Paste multiple CDR3/peptide/MHC queries and let the backend return compact CROSSTCR match summaries without loading the full release tables into the browser.

CSV / TSV paste Backend lookup CSV export

Batch input

Lookup scope

Parsed rows{{ batchParsedRows.length }}

Maximum submitted{{ batchMaxRows }}

Accepted columnsCDR3_alpha, CDR3_beta, Peptide, MHC_Allele

Header rows are recommended. Without headers, columns are interpreted as alpha, beta, peptide, MHC allele, and optional label.

#	CDR3_alpha	CDR3_beta	Peptide	MHC
{{ row.index + 1 }}	{{ row.alpha \|\| '-' }}	{{ row.beta \|\| '-' }}	{{ row.peptide \|\| '-' }}	{{ row.mhc \|\| '-' }}

Query	Dataset	Records	Groups	TCRs	pMHC context
{{ row.label }} {{ row.query }}	{{ row.dataset }}	{{ row.records }}	{{ row.groups }}	{{ row.tcrs }}	{{ row.peptides }} peptide(s), {{ row.mhcAlleles }} MHC allele(s)

Priority 5

CROSSTCR Query Builder

Build precise links into Dataset and Network from paired TCR sequences, peptide ligands, and MHC alleles without manually composing URL parameters.

Dataset link Network link Backend counts

Dataset view

CDR3_alpha

CDR3_beta

Peptide

MHC allele

Generated actions

Open matching records directly, or ask the backend for compact match counts.

Dataset scope{{ queryLocalSummary.dataset }}

Current query{{ queryLocalSummary.normalized || '-' }}

Lookup status{{ queryLocalSummary.status }}

Open Dataset Open Network

Dataset links support field-level filters. Network links pass the same parameters and are ready for URL-aware network loading.

{{ dataset.records }}records

{{ dataset.groups }}groups

{{ dataset.tcrs }}TCRs

Priority 1

pMHC Context Helper

Summarize the database context around a peptide-MHC query, including matched records, cross-reactive groups, linked TCRs, clinical contexts, and source annotations.

Peptide MHC allele Compact preview

Peptide MHC allele

Open Dataset

Local summary

Peptide length{{ pmhcLocalSummary.length || '-' }}

Query type{{ pmhcLocalSummary.type }}

MHC class guess{{ pmhcLocalSummary.mhcClass }}

Normalized query{{ pmhcLocalSummary.normalized || '-' }}

Backend lookup uses cached release JSON and returns only compact summaries, so the browser does not need to load the full datasets.

{{ dataset.records }}records

{{ dataset.groups }}groups

{{ dataset.tcrs }}TCRs

Peptide	MHC	CDR3_beta
{{ row.Peptide }}	{{ row.MHC_Allele }}	{{ row.CDR3_beta }}

Priority 4

Sequence Distance Calculator

Input amino-acid sequences and compute pairwise distance or similarity matrices using edit distance, k-mer overlap, BLOSUM62 alignment, and amino-acid frequency vectors.

CSV export Alignment view No server upload

Input sequences one per line

Letters are uppercased; blank lines are ignored.

Metrics

Levenshtein Hamming k-mer Jaccard BLOSUM62 NW Euclidean Manhattan Cosine

k-mer length

Gap open

Gap extend

Show BLOSUM alignment

Enter at least two sequences.

#	S{{idx+1}}
S{{i+1}}	{{ fmt(val) }}

Hamming applies to equal-length pairs only. Jaccard distance is computed on k-mers. BLOSUM62 uses affine Needleman-Wunsch alignment normalized by self-similarity. Euclidean, Manhattan, and Cosine are computed from 20-dimensional amino-acid frequency vectors.

Priority 6

Prediction Tools & External Links

A categorized catalog rebuilt from the supplemental material table, grouping tools by sequence similarity, structure modeling, ML/DL prediction, multimodal risk analysis, and selected external resources.

{{ stats.total }} total {{ stats.shown }} displayed {{ stats.minYear }}-{{ stats.maxYear }}

Tool Name {{ sortAsc ? '▲' : '▼' }} ⬍	Category {{ sortAsc ? '▲' : '▼' }} ⬍	Method	Input	Prediction Task	CR Use {{ sortAsc ? '▲' : '▼' }} ⬍	Year {{ sortAsc ? '▲' : '▼' }} ⬍	Reference
No matching tools found.
{{ tool.name }}	{{ tool.category_label }}	{{ tool.methodology }}	{{ tool.input }}	{{ tool.prediction_task }}	{{ tool.cross_reactivity_use }}	{{ tool.year }}	{{ tool.reference }}
Supplemental Source: {{ tool.supplemental_table }} Category: {{ tool.category_label }} Method: {{ tool.methodology }} Input Features: {{ tool.input }} Data Source: {{ tool.data_source \|\| '-' }} Prediction Task: {{ tool.prediction_task }} Cross-reactivity Use: {{ tool.cross_reactivity_use }} Reference: {{ tool.reference }} Interpretation: {{ tool.category_description }}

Selected External Resources Quick links

Common external tools are organized by practical use case so users can move from CROSSTCR records to specificity prediction, structure modeling, or peptide mimicry checks.

Priority 3

TCR Numbering & CDR3 Annotation

Annotate curated CDR3 alpha/beta strings directly, or submit full TRA/TRB variable-domain sequences for backend-priority ANARCI numbering with local fallback.

CDR3-level Backend numbering JSON export

CDR3 inputs

CDR3_alpha CDR3_beta

V_alpha

J_alpha

V_beta

J_beta

Open Dataset

CDR3 interpretation

This mode is appropriate for CROSSTCR records because the release stores curated CDR3 strings and V/J annotations. It does not infer CDR1/CDR2 or framework residues.

Alpha length{{ numberingCdr3Analyses[0].length || '-' }}

Beta length{{ numberingCdr3Analyses[1].length || '-' }}

Alpha V/J{{ numberingVAlpha || '-' }} / {{ numberingJAlpha || '-' }}

Beta V/J{{ numberingVBeta || '-' }} / {{ numberingJBeta || '-' }}

Sequence{{ chain.sequence || '-' }}

Length{{ chain.length || '-' }}

Length class{{ chain.lengthClass }}

Canonical C-start{{ chain.startsWithC }}

Common terminal residue{{ chain.commonTerminal }}

Residue-level CDR3 table

Chain	CDR3 position	Residue	Suggested use
{{ row.chain }}	{{ row.position }}	{{ row.residue }}	{{ row.role }}

Backend numbering calls ANARCI first for full TRA/TRB variable-domain sequences. If ANARCI is unavailable, CROSSTCR returns a clearly marked provisional local mapping so the page remains usable.

{{ numberingStatus && numberingStatus.anarciAvailable ? 'ANARCI ready' : 'Fallback active' }} {{ numberingStatusMessage }}

Full variable-domain input

TRA variable-domain sequence TRB variable-domain sequence

Anchors and actions

Alpha CDR3 anchor

Beta CDR3 anchor

Scheme

{{ chain.chain }} result {{ chain.status }}

Sequence length{{ chain.sequenceLength || '-' }}

CDR3{{ chain.cdr3 ? chain.cdr3.sequence : '-' }}

CDR3 source{{ chain.cdr3 ? chain.cdr3.source : '-' }}

Scheme{{ chain.scheme }}

{{ region.name }} {{ region.start }}-{{ region.end }} · {{ region.length }} aa

Index	Residue	Region	Numbering position
{{ row.index }}	{{ row.residue }}	{{ row.region }}	{{ row.position }}

Tools Hub

Batch Query / Batch Annotation

CROSSTCR Query Builder

Generated actions

{{ dataset.label }}

pMHC Context Helper

Local summary

{{ dataset.label }}

Sequence Distance Calculator

Prediction Tools & External Links

{{ tool.name }}

TCR Numbering & CDR3 Annotation

CDR3 inputs

CDR3 interpretation

Residue-level CDR3 table

Full variable-domain input

Anchors and actions

Tools Hub

Batch Query / Batch Annotation

CROSSTCR Query Builder

Generated actions

{{ dataset.label }}

pMHC Context Helper

Local summary

{{ dataset.label }}

Sequence Distance Calculator

Prediction Tools & External Links

{{ tool.name }}

TCR Numbering & CDR3 Annotation

CDR3 inputs

CDR3 interpretation

Residue-level CDR3 table

Full variable-domain input

Anchors and actions

Global Alignment (Affine NW)