prolineconcepts:protscoring
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prolineconcepts:protscoring [2014/01/24 12:12] 132.168.72.206 |
prolineconcepts:protscoring [2015/07/10 15:21] (current) 132.168.72.225 [Proteins and Proteins sets scoring] |
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| ====== Proteins and Proteins sets scoring ====== | ====== Proteins and Proteins sets scoring ====== | ||
| - | There are multiple algorithms than could be use to calculate the Proteins and Protein Sets score. | + | There are multiple algorithms than could be used to calculate the Proteins and Protein Sets score. |
| - | Proteins score are computed during the importation phase while Protein Sets score are comptued during the validation phase. | + | Proteins score are computed during the importation phase while Protein Sets score are computed during the validation phase. |
| ===== Protein ===== | ===== Protein ===== | ||
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| * importing Mascot result file : the Mascot standard scoring is used (sum of peptide matches scores) | * importing Mascot result file : the Mascot standard scoring is used (sum of peptide matches scores) | ||
| * importing OMSSA result file : FIXME | * importing OMSSA result file : FIXME | ||
| + | * importing X! tandem result file : the X! Tandem standard hyperscore is used | ||
| ===== Protein Set ===== | ===== Protein Set ===== | ||
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| ==== Mascot MudPIT Scoring ==== | ==== Mascot MudPIT Scoring ==== | ||
| - | This is scoring scheme is also based on the sum of all non-duplicate peptide matches score. However the score for each peptide match is not its absolute value, but the amount that it is above the threshold: the score offset. Therefore, peptide matches with a score below the threshold do not contribute to the protein score. Finally, the average of the thresholds used is added to the score. For each peptide match, the "threshold" is the homology threshold if it exists, otherwise it is the identity threshold. | + | This scoring scheme is also based on the sum of all non-duplicate peptide matches score. However the score for each peptide match is not its absolute value, but the amount that it is above the threshold: the score offset. Therefore, peptide matches with a score below the threshold do not contribute to the protein score. Finally, the average of the thresholds used is added to the score. For each peptide match, the "threshold" is the homology threshold if it exists, otherwise it is the identity threshold. |
| The algorithm below illustrates the MudPIT score computation procedure: | The algorithm below illustrates the MudPIT score computation procedure: | ||
prolineconcepts/protscoring.1390561941.txt.gz · Last modified: 2014/01/24 12:12 by 132.168.72.206
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