PHIRE Software

From:

PHIRE (PHage In silico Regulatory Elements)


" .. a program that scans bacteriophage genomes to extract potential conserved regulatory elements including phage promoters, terminators and regions involved in genome replication".

Typical examples of such genome-specific targets are phage-specific promoters.


Since these elements can often be seen as sets of conserved sequence strings contained within the genome of length G, the PHIRE algorithm systematically compares all the DNA substrings of a specified length (L) to one another, allowing a limited number of mismatches (degeneracy D) to sort out and extract the largest sets (DominantNum) of substrings that represent a unique consensus.

In this manner, the entire genome is analysed on both the direct and complementary DNA strand to extract conserved subsequences with a substantial level of occurrence throughout the genome.

To visualize the sequences around the consensus sequence, the window size (W) can be adapted to include the sequences left and right of each selected DNA individual string."


These are the results extract by PHIRE with D29 mycobacteriophage genome.
I have highlighted by violet colour the leading sequence.

D29 mycobacteriophage
(by PHIRE software)

TCGCTCGGTGGCTGTCAACC 48417- 48436 w

CTAGTCGGTGGCTGTCAAGC 48290- 48309 w

TTTCTCGGTGGCTGTCAAGT 47607- 47626 w

CCCTTCGGTGGCTGTCAAGT 47501- 47520 w

GGTCACGGTGTCTGTCAAGT 47235- 47254 w

TCTGCGGGTGGCTGTCAAGT 44036- 44055 w

CCTCTTGGTGGCTGTCAAGT 43738- 43757 w

CTGGTTGGTGGCTGTCAAGT 41872- 41891 w

CCTTTCGGTGGCTGTCAAGG 41320- 41339 w

TCGCTCGGTGGATGTCAAGT 40275- 40294 w

GATGCCGGTGGCTGTCAAGT 39110- 39129 w

CAGCTTGGTGGCTGTCAAGT 36773- 36792 w

CCTCCCGGTGGATGTCAAGT 13077- 13058 c

TTTCGTGGTGGCTGTCAAGT 04698- 04679 c



I have used PHIRE with L5, BxZ2 and TM4 genomes.

In all genome sequences I have highlighted the D29 genome leading sequence by violet color:

GGTGGCTGTCAAGT

Again we have the confirmation that D29 mycobacteriophage is derived from L5 mycobacteriophage.

L5 (GGTGGCTGTCAAGT)

TTCGGTGGCTGTCAAGCGGG 51453- 51472 w

TTCGGTGGCTGTCAAGTCTC 50768- 50787 w

GTCGGTGGCTGTCAAGTCAG 50662- 50681 w

TTCGGTGGCTGTCAAGTTGT 50395- 50414 w

CACGGTGTCTGTCAAGTCAG 50128- 50147 w

ATCGGTGGCTGTCAAGGTGA 42948- 42967 w

CTCGGTGGCTGTCAAGTTGG 42589- 42608 w

TTTGGTGGATGTCAAGTTAG 40771- 40790 w

CTCGGTGGCTGTCAAGTCGG 40297- 40316 w

CCTGGTGGATGTCAAGTTCG 38783- 38802 w

CTTGGTGGCTGTCAAGTTCT 36250- 36269 w

CTCCTCGGCTGTCAGGTTGG 36032- 36051 w

CTCGGTGGATGTCAAGTAGT 32429- 32448 w

TTCGGTGGCTGTCAAGTTGT 28664- 28683 w

CCGGGTGGCTGTCAAGTTGG 14895- 14876 c

TCGGGTGGATGTCAAGTTGG 04570- 04551 c

BXZ2 ( GGTGGCTGTCAAGT)

TTCCCGTTCTCTGTCAAGCC 50473- 50492 w

ATTCGGTTCTCTGTCAAGTC 50381- 50400 w

CGTCTGTTCTCTGTCAAGTG 50244- 50263 w

CGTTCGTTCTCTGTCAAGTC 50186-50205 w

CTTTCGGTCTCTGTCAAGTC 49721- 49740 w

GCTCCGTTCTCTGTCAAGTC 49269- 49288 w

CTTCTGTTCTCTGTCAAGTC 48523- 48542 w

CCTTCGTTCTCTGTCAAGTA 43249- 43268 w

ACTCCGTTCTCTGTCAAGTA 42427- 42446 w

CTTTCGTTCTCTGTCAAGTA 41216- 41235 w

CCTCCGTTCTCTGTCAAGTG 39160- 39179 w

ATCTTGTTCTCTGTCAAGTG 36950- 36969 w

CCTCCGTTCTCTGTCAAGTC 33286- 33305 w

TCTCTGTTCTCTGTCAAGTG 30053- 30072 w

TCTCAGTTCTCTGTCAAGTC 07039- 07020 c

CTTTCGTTATCTGTCAAGTG 04252- 04233 c

TM4 (GGTGGCTGTCAAGT)

CGTCGCCGAGCTGGCCGCGG 02047- 02066 w

CATCACCAAGCTGGCCTCGG 03375- 03394 w

CGACGCCGAGCTGGGCAAGG 04423- 04442 w

CGTGGCCGTGCTGACCGAGG 06304- 06323 w

CGTCGACGAGCCGGTGGCGG 09370- 09389 w

CGGCGCCACGCTGGCCGCGA 11407- 11426 w

CGACGACGAGCTGGCGGGGG 17123- 17142 w

CAGCGCCGACCCGGCCGCGG 18313- 18332 w

CATCGACGAGCTGGCGGCGT 19008- 19027 w

CGTCGCCGTGATCGCCGCGA 27345- 27364 w

GATCGACGAGCTGGCGGCGG 28482 28501 w

GCTCGCCGACCTGGCCGCGT 36708- 36727 w

CGTCACCCGGCTGGCCGCGG 41785- 41804 w

CGTCGGCCAGCGGGTCGCGG 47532- 47551 w

GTCCGCCGAGCAGTACCCGG 49485- 49504 w

AGCCGCCGAGCTGGCGGCCG 52585 52604 w

AGTCGCCGAGCGAGCTGCGG 46575- 46556 c

TGCCGACGAGCTGGCGGCGG 45625- 45606 c

CGTCGACGACCTGGCCGCCG 45163- 45144 c

CGTCGGCGAGCTGGTCGTCG 39811- 39792 c

CATCGCCGAGCGGGCCTCGC 33269- 33250 c

CGGTGCCGTGCTGGCCGCCG 31087- 31068 c

GCTCGCCGAGCTGGCCGCCG 21841- 21822 c

TCTCGCCGAGCTTGCCGCTG 11342- 11323 c

AGGCGCCGAGCTGCTCGCGG 02191- 02172 c