MAFFT

Align multiple amino acid or nucleotide sequences.

Workflow

1. Input multi-FASTA sequences
   Upload a FASTA file containing multiple nucleotide or protein sequences.

2. Run multiple sequence alignment
   Use MAFFT automatic strategy selection to align all input sequences.

3. Calculate alignment statistics
   Summarize input sequence number, sequence length range, alignment length, total gap characters, and gap ratio.

4. Generate alignment output
   Output the aligned FASTA file and an alignment summary table.

Data

The MAFFT sample dataset contains predicted ORF sequences from a single sample, sampleA, including amino acid sequences (sampleA.orf_100nt.faa) and corresponding nucleotide sequences (sampleA.orf_100nt.ffn). These sequences are used to demonstrate redundancy removal and representative gene catalog construction by CD-HIT clustering.

Result

v0.1: The pipeline is stored in Code Repository: CRS1242177572100648960. The computational docker enrionment is stored in Software Repository: SRS1242177610507890688.

Reproducibility

The pipeline utilizes code CRS1225977902999547904 and Docker image SRS1225987480378159104, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'MAFFT'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.