msa_set_scoreSA: Compare Reference MSAs with Alternative MSAs
In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description Usage Arguments Value Author(s) References See Also

Wrapper function for program msa_set_score v2.01 of the GUIDANCE program (see reference). Copyright: To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: talp@post.tau.ac.il. Please note that the use of the GUIDANCE program is for academic use only. C code computing basic MSA comparision. The most basic is the residue pairs residue score, which checks if residue pairs combinations are correctly aligned in both MSAs. From this the residue score, residue column score (GUIDANCE score), residue sequence score are computed. It also calulates the column score (CS), which simply checks if a column is identically aligned in the alternative MSA.

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msa_set_scoreSA(ref, alt,
  exec = "/Users/krah/Documents/R/pkgs/polenta/src/msa_set_score_src/msa_set_score",
  bootstrap)

`ref`	of class data.frame, is the reference MSA ('BASE MSA') with sequences as columns
`alt`	path to alternative files
`exec`	XXX.
`bootstrap`	XXX.

list containing following scores:

mean_scores: residue pair score and mean column score

column_score: identically aligned columns are asigned 1, otherwise 0; if more than one alternative MSA is supplied then mean of this score

residue_column_score: if one alternative MSA is supplied, then this is the SPC (sum-of-pairs column score); if more than one this is the average of the SPCs of all MSAs. The SPC is the mean over all residue pair scores (see there) in a column. This is also refered to as the GUIDANCE score.

residue_pair_score: if one alternative MSA is supplied then this is 1 if a residue pair was identically aligned as in the reference MSA and 0 otherwise. If more than one, then the average of the residue pair scores that result from each comparison with the reference MSA.

residue_pair_residue_score: calculated by averaging the residue column score over all pairs that have this residue. This is a confidence score for each residue.

residual_pair_sequence_pair_score_ if one alternative MSA is supplied this compares residue pairs of all sequence pairs of the base MSA with the reference MSA and returns 1 if identical and 0 if not and then averages over all pairs of a sequence pair. If more than one the the mean over those averages are computed.

residual_pair_sequence_score: like the residue_column_score but for sequences

Franz-Sebastian Krah

Penn et al. (2010). An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.

guidance, guidance2, HoT

heibl/polenta documentation built on May 17, 2019, 3:22 p.m.