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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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Support blast and diamond blastp for ortholog identification #643

Closed Tong-Chen closed 2 months ago

Tong-Chen commented 2 months ago

As compared, using blastn generated the least anchors. diamond blastp is 6 times faster than blast+ blastp with similar aligning results.

# numbers represent the number of lines in each result file.

diamond blastp

    8179 ./diamond/result/01_jcvi_ortholog/Aan1.Abu1.lifted.anchors
       7 ./diamond/result/01_jcvi_ortholog/Aan1.Aar1.anchors.simple
   23118 ./diamond/result/01_jcvi_ortholog/Aan1.Aar1.anchors
     533 ./diamond/result/01_jcvi_ortholog/Aan1.Aca1.lifted.anchors
     397 ./diamond/result/01_jcvi_ortholog/Aan1.Aca1.anchors
    5226 ./diamond/result/01_jcvi_ortholog/Aan1.Abu1.anchors
   41463 ./diamond/result/01_jcvi_ortholog/Aan1.Aar1.lifted.anchors
       4 ./diamond/result/01_jcvi_ortholog/Aan1.Abu1.anchors.simple

blast+ blastp

    8258 ./blastp/result/01_jcvi_ortholog/Aan1.Abu1.lifted.anchors
       5 ./blastp/result/01_jcvi_ortholog/Aan1.Aar1.anchors.simple
   22879 ./blastp/result/01_jcvi_ortholog/Aan1.Aar1.anchors
     488 ./blastp/result/01_jcvi_ortholog/Aan1.Aca1.lifted.anchors
     357 ./blastp/result/01_jcvi_ortholog/Aan1.Aca1.anchors
    5213 ./blastp/result/01_jcvi_ortholog/Aan1.Abu1.anchors
   41708 ./blastp/result/01_jcvi_ortholog/Aan1.Aar1.lifted.anchors
       3 ./blastp/result/01_jcvi_ortholog/Aan1.Abu1.anchors.simple

last

    6876 ./nucl/result/01_jcvi_ortholog/Aan1.Abu1.lifted.anchors
       5 ./nucl/result/01_jcvi_ortholog/Aan1.Aar1.anchors.simple
   21811 ./nucl/result/01_jcvi_ortholog/Aan1.Aar1.anchors
     318 ./nucl/result/01_jcvi_ortholog/Aan1.Aca1.lifted.anchors
     241 ./nucl/result/01_jcvi_ortholog/Aan1.Aca1.anchors
    4548 ./nucl/result/01_jcvi_ortholog/Aan1.Abu1.anchors
   38615 ./nucl/result/01_jcvi_ortholog/Aan1.Aar1.lifted.anchors
       4 ./nucl/result/01_jcvi_ortholog/Aan1.Abu1.anchors.simple

blast+ blastn

      18 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Abu1.lifted.anchors
       5 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Aar1.anchors.simple
   22076 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Aar1.anchors
      18 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Aca1.lifted.anchors
      16 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Aca1.anchors
      13 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Abu1.anchors
   33157 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Aar1.lifted.anchors
       1 ./nucl_blastn/result/01_jcvi_ortholog/Aan1.Abu1.anchors.simple