I'm trying to extract prophages from bacterial genomes, the principal issue i been having is that i have multiple hits distributed along bacterial genomes and i don't know how to extract them together in order to get the complete prophage genome. I know that there is an outfmt of blast that can give me subjetct-sart and subjetct-end but i want to know if there is an alternative that can give me only the initial and final positions.
In the example only two strains are shown, those contain several hits for one bacteriophage, i want to retrieve the initial and final position of those hits to extract the prophage from databases
Thanks.
You don't need to blast, there are several software available for this task
- Sousa et al, 2018;PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes;Frontiers in Genetics;DOI=10.3389/fgene.2018.00644
- Song et al, 2019; Prophage Hunter: an integrative hunting tool for active prophages, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W74–W80, https://doi.org/10.1093/nar/gkz380
- Starikova et al, 2019; Phigaro: high throughput prophage sequence annotation; bioRxiv preprint ; doi: http://dx.doi.org/10.1101/598243.
- Akhter et al, 2012; PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies; Nucleic Acids Res. 2012 Sep; 40(16): e126.
- Reis-Cunha et al, 2017; ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database. bioRxiv preprint; doi: http://dx.doi.org/10.1101/176750.
Also, check
https://omictools.com/prophage-prediction-category
You don't need to blast, there are several software available for this task
- Sousa et al, 2018;PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes;Frontiers in Genetics;DOI=10.3389/fgene.2018.00644
- Song et al, 2019; Prophage Hunter: an integrative hunting tool for active prophages, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W74–W80, https://doi.org/10.1093/nar/gkz380
- Starikova et al, 2019; Phigaro: high throughput prophage sequence annotation; bioRxiv preprint ; doi: http://dx.doi.org/10.1101/598243.
- Akhter et al, 2012; PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies; Nucleic Acids Res. 2012 Sep; 40(16): e126.
- Reis-Cunha et al, 2017; ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database. bioRxiv preprint; doi: http://dx.doi.org/10.1101/176750.
Also, check
https://omictools.com/prophage-prediction-category
You can use PHASTER to extract the full sequences. If you have multiple genomes try de API of PHASTER or Phispy. Both tools will give you the starting and ending coordinates of all detected prophage regions.
Article PHASTER: a better, faster version of the PHAST phage search tool
Article PhiSpy: A novel algorithm for finding prophages in bacterial...
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