About Tox|Note:

Tox|Note -the spider toxin annotation and evaluation facility- is a bioinformatic pipeline that aims to fast-track the analysis of venom-gland transcriptomes generated by next-generation sequencing projects. The Tox|Note pipeline is designed with a user-friendly interface so users can achieve the following tasks with minimal manual input: a) annotation of toxin transcripts (Tox|Blast/Tox_Seek|) b) prediction of signal peptide and propeptide cleavage sites in full-length spider-toxin precursors (Spider|ProHMM) and c) automatic generation of rational toxin names (Tox|Name) based on published nomenclature rules (King et al., 2008).

Tox|Note also incorporates tools developed by the European Molecular Biology Laboratory (EMBL), the European Bioinformatics Institute (EBI), and the Australian Bioinformatics Resource (EMBL-ABR) (under the Tox|Submission tab).

IMPORTANT NOTES:

1) Tox|Blast

1.1 To use Tox|Blast, register by sending an email to: support@arachnoserver.org

1.2 Tox|Blast requires the following input files: a FASTA file containing the contig/singlet consensus sequences produced by any assembly software (e.g., Newbler, MIRA, VELVET/OASES, Trinity, etc). Please note that the use of symbols in the headers and their length are important features and may create errors while parsing the input file. We recommend avoidance of long descriptions and symbols in uploaded FASTA files, especially the use of pipes in headers. If your header looks like the following example: >TR1|c0_g1_i1 len=509 path=[512:0-391 513:392-415 514:416-508] [-1, 512, 513, 514, -2], please make sure you cut the description and remove the pipe symbol, so the header would be: >TR1_c0_g1_i1 .

2) Tox|Submission

If you are planning to submit sequencing experiments done with Illumina, send us an email to: support@arachnoserver.org. Currently, uploading Illumina fastq and BAM files is not supported by our Tox|Submission page.

Please refer to the User Manual For further details on how to use Tox|Note