itaxotools-blastax 1.0.0

Run BLAST, parse hits and more

BlasTax

A graphical user interface to run BLAST and parse hits:

• Make BLAST database: Create a BLAST database from a sequence file
• Regular BLAST: Find regions of similarity between sequences in a query file and a BLAST database
• BLAST-Append: Append the aligned part of matching sequences to the original query sequences
• BLAST-Append-X: Like BLAST-Append, but appends nucleotides c orresponding to the protein database
• Decontaminate: Remove contaminants from query sequences based on two ingroup and outgroup databases
• Decontamination by taxonomy: Filter query sequences based on BLAST matches and taxon IDs
• Assign taxonomy: Assign taxonomic information to each query sequence based on the best BLAST hit
• Museoscript: Create sequence files from BLAST matches
• Database operations: Extract sequences from a BLAST database and save them in FASTA format

The program also includes a variety of tools for processing FASTA files:

• Fast prepare: Rename FASTA sequence identifiers in preparation for BLAST analysis
• Fast split: Split large sequences or text files into smaller files
• Fast merge: Merge multiple sequences or text files into a single large file
• Group merge: Merge FASTA files by filename
• Removal of stop codons: Remove stop codons from a dataset
• Codon trimming: Trim coding sequences to start with first codon position

Some extra tools are also available:

• SCaFoSpy: Create chimerical sequences for species
• Protein translator: Generate protein translations for each sequence
• MAFFT alignment: Multiple sequence alignment using MAFFTpy
• Codon-aware alignment: Align nucleotide sequences as proteins without altering codons
• Cutadapt: Remove adapter sequences and quality trimming

Input sequences must be in the FASTA or FASTQ file formats.

Executables

Download and run the standalone executables without installing Python or BLAST+.

Installation

BlasTax is available on PyPI and can be installed using pip:

pip install itaxotools-blastax

After installation, run the program with:

blastax

If the BLAST+ binaries are not found in your system PATH at runtime, the program will prompt you to automatically download them to your system-specific configuration directory (under iTaxoTools/BlasTax, see platformdirs).

To reset the location where the program looks for BLAST+, run:

blastax --reset

Citations

BlasTax was developed in the framework of the iTaxoTools project:

Vences M. et al. (2021): iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. - Megataxa 6: 77-92.

Code by Nikita Kulikov, Anja-Kristina Schulz and Stefanos Patmanidis.

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BlasTax integrates the BLAST+ suite from NCBI:

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.

Cutadapt is included as a Python module to remove adapter sequences from high-throughput sequencing reads:

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10-12.

Museoscript was rewritten following the original concept of the Linux bash script:

Rancilhac, L., Bruy, T., Scherz, M. D., Pereira, E. A., Preick, M., Straube, N., Lyra, M. L., Ohler, A., Streicher, J. W., Andreone, F., Crottini, A., Hutter, C. R., Randrianantoandro,J. C., Rokotoarison, A., Glaw, F., Hofreiter, M. & Vences, M. (2020). Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus). Journal of Natural History, 1-32.

MAFFT is a multiple sequence alignment program that was integrated using MAFFTpy:

Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059-3066.