How to use the Sequence Character Indexer tool
This tool lists every position in a sequence with its character and a type label (heuristic rules for DNA / RNA / protein / other). Load data from NCBI, a file, or paste text, then analyze in your browser. Export the full index as CSV when needed.
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Choose input. Use tabs: NCBI Accession (enter an ID and Fetch Sequence), Upload File (FASTA or plain text—drag-and-drop or browse; GenBank flat files are not fully parsed—prefer FASTA or raw sequence), or Direct Input (paste sequence). Analyze Sequence enables once a sequence is ready.
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Analyze. Click Analyze Sequence to build the index. Summary cards show total length, unique characters, and GC content (where applicable).
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View mode. Switch Grid View (two columns with position cells), Table View (position / character / type), or Compact View. In grid mode, use Grid Density (Normal, Compact, Expanded) and Zoom on a section for a larger modal view.
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Pagination. Set Items per page (500–5000) and use Previous / Next for long sequences so the browser stays responsive.
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Export. Click Export as CSV to download the indexed positions for use in spreadsheets or scripts.
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Citation. APA, MLA, and BibTeX strings are under How to Cite at the bottom of this tool (below the FAQ).
Scope: Type labels follow simple letter rules—they do not replace experimental assay of molecule class. Very long sequences can still stress low-memory devices; reduce page size or work with a subsequence. Clear All resets inputs. For research and teaching, not clinical use.
Frequently Asked Questions
What are the latest features of the Sequence Indexer?
The Sequence Indexer now supports a two-column grid layout, zoomable sequence sections, grid density controls, responsive design for mobile/tablet, and advanced input/output options. You can analyze sequences from NCBI, upload files, or paste text, and view results in multiple formats.
How does the two-column grid and zoom feature work?
The main grid displays your sequence in two columns per row, each showing 100 positions. Each column has a Zoom button (🔍) that opens a detailed modal view for that section, making it easy to examine specific regions in depth.
What is grid density control?
Grid density controls let you switch between Normal, Compact, and Expanded views. This changes the number of columns and font size, so you can see more or less data per screen depending on your preference.
How does the tool handle very large sequences?
The tool uses pagination: only the current page of positions is drawn in the grid or table (you choose 500, 1000, 2000, or 5000 per page). Use Previous / Next to move through the sequence. Zoom works on whichever section you are viewing. The full sequence is kept in memory in your browser, so extremely large inputs may still be heavy on low-memory devices.
What sequence formats and sources are supported?
You can input sequences by:
- NCBI Accession ID (e.g., NC_045512.2, NM_000546.6)
- File Upload — FASTA or plain sequence text (lines starting with
> are treated as FASTA headers). Standard GenBank flat files are not parsed; export FASTA from NCBI or paste the raw sequence.
- Direct Text Input
The summary
Type line uses the proportion of DNA-like (ATGC), RNA-like (AUGC), or protein-like letters in the sequence.
Per-position colors use the same kind of rules on each character (letters like A, G, C are ambiguous between DNA and protein). Accession IDs are not used to color the grid.
How does the responsive design help on mobile and tablet?
The layout automatically adapts to your device. On smaller screens, the grid switches to a single column, buttons and controls stack vertically, and the modal view remains easy to use. All features are fully accessible on mobile and tablet.
How can I export or share my results?
Use the Export as CSV button to download your full sequence analysis as a spreadsheet. The export includes all positions, characters, and types, regardless of the current page or view.
What do the color codes mean in the grid?
In grid and zoom views, each cell uses a background tint: DNA (blue tint), RNA (green tint), protein (red tint), and other (gray). In table view, the character itself is colored (blue / green / red / gray). Hover or the tooltip shows position and type.
Is my sequence data private?
Yes. After your sequence is loaded, indexing and display run in your web browser. Pasted text and uploaded files are read locally and are not sent to us for storage. For NCBI fetch, only the accession ID is sent to this site’s server to proxy the public record from NCBI; the response is returned to your browser and is not stored for reuse.
Who can I contact for support or suggestions?