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Table 1 Overall memory usage. Overall memory usage required to process all proteins with a signal peptide in Mb.

From: Decoding HMMs using the k best paths: algorithms and applications

 

Probability only

Tree-based

Matrix-based

k = 100

4

8

290

k = 200

6

13

570

k = 300

7

17

850

k = 400

8

21

1130

  1. This value corresponds to the memory required for the longest protein. 'Probability only' corresponds to a run where no backtracking was performed, 'Tree-based' refers to our tree-based implementation, 'Matrix-based' refers to naive matrix approach.
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BMC Bioinformatics

ISSN: 1471-2105

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