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hoelzer / pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
GNU General Public License v3.0
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finalize blast-diamond switch #12

Closed hoelzer closed 1 year ago

hoelzer commented 1 year ago

Motivated by a PR from @michoug #11 blast is exchanged by diamond due to faster speed and similar results.

hoelzer commented 1 year ago

Old Results using blast and v2.0.1:

ID Cav_10DC88 Cga_08-1274-3 Cmu_Nigg Cps_6BC Ctr_D-UW-3-CX
Cav_10DC88 100.0 96.8074 83.3151 90.5553 83.9782
Cga_08-1274-3 96.8074 100.0 83.6313 90.4182 84.2515
Cmu_Nigg 83.3151 83.6313 100.0 82.718 96.3984
Cps_6BC 90.5553 90.4182 82.718 100.0 82.7292
Ctr_D-UW-3-CX 83.9782 84.2515 96.3984 82.7292 100.0

New Results using diamond in blastp mode:

ID Cav_10DC88 Cga_08-1274-3 Cmu_Nigg Cps_6BC Ctr_D-UW-3-CX
Cav_10DC88 100.0 96.7532 82.6586 90.0363 83.6512
Cga_08-1274-3 96.7532 100.0 83.5196 90.0476 84.1402
Cmu_Nigg 82.6586 83.5196 100.0 82.3435 96.2859
Cps_6BC 90.0363 90.0476 82.3435 100.0 82.1962
Ctr_D-UW-3-CX 83.6512 84.1402 96.2859 82.1962 100.0