PDB to FASTA

This tool extracts protein/nucleotide sequences from PDB files.

PDB: 1rv1.pdb

Output (FASTA)

>1RV1:A UNP:Q00987 MDM2_HUMAN
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
LFGVPSFSVKEHRKIYTMIYRNLVV
>1RV1:B UNP:Q00987 MDM2_HUMAN
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
LFGVPSFSVKEHRKIYTMIYRNLVV
>1RV1:C UNP:Q00987 MDM2_HUMAN
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
LFGVPSFSVKEHRKIYTMIYRNLVV
1
>1RV1:A UNP:Q00987 MDM2_HUMAN
2
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
3
LFGVPSFSVKEHRKIYTMIYRNLVV
4
>1RV1:B UNP:Q00987 MDM2_HUMAN
5
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
6
LFGVPSFSVKEHRKIYTMIYRNLVV
7
>1RV1:C UNP:Q00987 MDM2_HUMAN
8
ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
9
LFGVPSFSVKEHRKIYTMIYRNLVV
10

The extracted FASTA.

See also

FASTQ to FASTA - Convert FASTQ files to FASTA format.

ABI to FASTA - Convert AB1 files (Applied Biosystems/ABI trace files) to FASTA format.

GenBank to FASTA - Convert GenBank flat files to FASTA format.

Sequence Logo Generator - Create sequence logos from FASTA alignments.

Sequence Alignment Viewer - Open FASTA files in the browser.

What is FASTA and how is it used? - Learn about the FASTA format and its applications.

FASTA Parse Tree Viewer - Visualize the parse tree of FASTA files.

FASTA Editor - A simple online editor for biological sequences in the FASTA format.

PDB Editor - A simple online editor for Protein Data Bank (PDB) files.

The RDF model of the Gene Ontology, demystified - An outline of the structure of the Gene Ontology RDF graph and ways to query it.

BLAST WASM (In-browser NCBI BLAST) - Compiling the BLAST sequence search/alignment tool to WASM.

DESeq2 in the browser - Running DESeq2 in the browser.

Phylogenetic Tree Builder - Reconstruct phylogenetic trees from protein or DNA/RNA sequence alignments.

Genome Browser - Explore the human genome.

Phylogenetic Tree Editor - An online visual editor for phylogenetic trees.

Plasmid Map Generator - A tool to generate plasmid maps from GenBank files.

NCBI Taxonomy Browser - A simple tool for viewing the NCBI taxonomy tree.

Newick Parse Tree Viewer - View the parse trees of Newick strings.

3D Mol Viewer - View molecular models in 3D.

Scalable genomic alignment with Progressive Cactus - How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.

The ambitious challenge of finishing the human genome - Generating a complete human genome sequence, chromosome by chromosome.

WikiPathways: A Wikipedia for biological pathways - An overview of the collaboratively edited structured pathway encyclopedia.

Bioinformatics Crossword - A daily crossword puzzle for bioinformatics terms.

FASTQ Editor - A simple online editor for biological sequences in the FASTQ format.

Newick Editor - A simple online editor for phylogenetic trees in the Newick format.

GenBank Flat File Editor - A simple online editor for the GenBank flat file format.

Clustal Editor - A simple online editor for Clustal multiple sequence alignment files.

PDBx/mmCIF Editor - A simple online editor for PDBx/mmCIF files.

EMBL Flat File Editor - A simple online editor for the EMBL flat file format.

Awesome bioinformatics - A curated list of awesome links, tutorials, and resources on bioinformatics and related topics.