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Home | Run AcaFinder | AcaFinder Results

There are several ways to utilize the AcaFinder website:

• (i) To understand the workflow behind AcaFinder, you may explore the Home pages
• (ii) To use AcaFinder and scan for potetnial Aca protein/operons in you genomic sequence of interest, go to Run AcaFinder page
• (iii) For external resources, go to Home Page.
• (iv) For introduction to the AcaFinder team, go to About
• (I) For an example out of AcaFinder, go to Example.

Welcome to AcaFinder! The Home page features an introduction to AcaFinder that discloses all incorporated bioinformatic tools, and a detailed outline of the AcaFinder workflow in a figure.

To input a genomic sequence for Aca screening, go to Run AcaFinder on the navigation bar. Sequence data can be submitted in two ways:

• Users can paste nucleotide/protein sequence in FASTA format in the submission box at top of page
• Users can upload a file containing FASTA-format nucleotide/protein sequences

**Data of ONE genome may be submitted at a time**

**Higher genomic assembly quality preferred**

Results are then displayed, where users can view where the Aca protein/operons are, and their associatin with prophages as well as CRISPR-Cas systems (if any)

Go to Run HMMsearch to only run your protein sequence/s of interest against our developed AcaHMMs(Aca Hidden Markov models)

The output of AcaFinder consists of the following:

• All Aca operons: Table of Aca operons and all associated prophage & CRISPR-Cas information from the AcaFinder's GBA approach
• All Aca-like proteins: Table of Aca-like proteins and all associated prophage & CRISPR-Cas information from the AcaFinder's Aca HMM approach
• Prophage Regions: Table of all prophage regions found
• Complete CRISPR Cas & Self-Targeting Spacers: Tables of all complete CRISPR-Cas systems found
• Genetic context of Aca operons (from GBA search): Circular graph of displaying Aca operons and associated information
• Genetic context of Aca-like proteins (from AcaHMM search): Circular graph of displaying Aca-like proteins and associated information

Table columns explained (All tables combined)

Operon Number: Operon ID of Aca operon identified

ProteinID: Protein ID of annotated protein

ContigID: ID of contig the protein resides

Protein Length: Length of protein

Start: Start position of protein

End: End position of protein

Acr Homologous: Acrs that share homology with protein

Potential Aca: Proteins found with HTH domains that could potentially be Aca proteins

AcaHMM HIT: Aca HMM model the protein share homology with

Pfam: Pfam database protein annotations

Complete CRISPR Cas and STSS: Complete CRISPR-Cas found, their type and location. Represented in the format of CONTIG|TYPE|Operon Start-End position|STSS info(STSS=spacer_name:spacer_location=>targeting_contig:targeting_location+spacer_name_2:spacer_location_2=>.../No_STSS)

Operon in Prophage: If protein in predicted prophage region, the column displays said predicted prophage region in the format of CONTIG:Prophage_location

Protein Sequence: Amino acid sequence of protein

Contig Length: Length of contig (nt) the protein resides

Aca HMM ID: Aca HMM model the protein share homology with

Aca-like Protein Coverage: Aca HMM model coverage of protein

Aca HMM Evalue: Aca HMM model evalue of protein hmmsearch

CRISPR Cas Type: Predicted type of CRISPR-Cas

Cas operon and location: ID and location of Cas operon (from CRISPRCasTyper, CRISPR_OperonID|Location_start-end)

CRISPR operon and location: ID and location of CRISPR operon (from CRISPRCasTyper, CRISPR_OperonID|Location_start-end)

STSS: Self-targeting information (spacer_name:spacer_location=>targeting_contig:targeting_location+spacer_name_2:spacer_location_2=>.../No_STSS)

If you have additional questions or comments regarding AcaFinder ,please do not hesitate to contact us .