We claim:
1. A computer-based method for determining whether or not a first peptide sequence database obtained by in silico tryptic digestion of a second peptide sequence database contains one or more peptide sequences that correspond to an experimental peptide prepared y tryptic digestion of a polypeptide, the method comprising executing the following steps by one or more automated computer algorithms without the intervention of an operator:
(a) analyzing a first fragmentation spectrum obtained by mass spectrometry of the experimental peptide to generate a first peak list comprising an assigned mass value for each of a plurality of peaks detected in the first fragmentation spectrum;
(b) interpreting the first peak list by a computer-mediated spectral read to construct one or more tripeptide search sequences (X) and deriving from the first peak list the following mass data: a mass (M1) of a sequence flanking the N-terminus of X, a mass (M2) of a sequence flanking the C-terminus of X, and a total mass, wherein each search sequence and associated mass data together constitute a search string (M1-X-M2), the one or more tripeptide search sequences being constructed by a computer-mediated process comprising performing the following steps in accordance with previously ordained criteria:
(i) interpreting the first peak list to deduce one or more tripeptide sequences within the experimental peptide;
(ii) selecting at least one deduced sequence by vectorial quality ranking;
(iii) permuting the deduced sequence or sequences to obtain a set of one or more permuted tripeptide sequences; and
(iv) constraining the set of one or more permuted sequences to obtain the one or more search sequences;
(c) searching the first database with at least one search string to determine whether the first database contains one or more candidate sequences that include a search sequence of a search string and are compatible with the mass data associated with that search string; and
(d) performing a computer-mediated back-read that tests the candidate sequences, if any, against a second peak list derived from the first fragmentation spectrum that contains at least one peak absent from the first peak list and determining whether one or more candidate sequences fit the data in the peak list according to one or more matching criteria, the back-read comprising:
(i) for each candidate sequence,
(1) identifying one or more amino acids flanking the search sequence (X) that is included in the candidate sequence;
(2) generating a list of theoretical mz values of at least one suite of ions for the identified flanking amino acids;
(3) comparing the theoretical mz values or corresponding assigned mass values with observed values in the first peak list or a second peak list derived from the first fragmentation spectrum and recording any matches that support the flanking amino acids; and
(ii) scoring the supported flanking amino acids and determining whether a candidate sequences satisfies the matching criteria,
wherein upon satisfaction of the matching criteria, the candidate sequences, if any, that satisfy the matching criteria are identified as corresponding sequences.
2. A computer-readable medium comprising instructions for causing a computer to perform the method according to claim 1.
3. A computer comprising instructions for performing the method according to claim 1.
4. A peptide or nucleic acid database comprising information obtained by performing the method according to claim 1.
5. A computer-readable file comprising information obtained by performing the method according to claim 1.
6. A display comprising information obtained by performing the method according to claim 1.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A computer-readable recording medium storing a program for use in FSM coverage measurement based on a language-described logical circuit and a test bench to direct a computer to perform:
extracting a FSM configuration from a language description and design information generated based on the language description;
expanding hierarchical levels of modules in a range of performing trace back from a variable as input of a FSM to output of a flip-flop or external input of a top module;
extracting FSM input logic between the hierarchical levels in response to input of a module;
detecting whether or not there is a state that is not reached or a transition that does not occur by an arithmetic result based on logic having exclusivity detected in the FSM input logic and a FSM transition logic; and
outputting a result of the detecting.
2. The recording medium according to claim 1, wherein:
the detecting detects by constant propagation whether or not there is a state that is not reached or a transition that does not occur according to an arithmetic result based on a constant propagation logic detected in the FSM input logic and the FSM transition logic.
3. The recording medium according to claim 1, wherein the computer is also directed to perform:
optimizing the expanding hierarchical levels and the extracting FSM input logic, and detects whether or not there is a state that is not reached or a transition that does not occur according to an arithmetic result based on the exclusive logic detected in the optimized FSM input logic and the FSM transition logic.
4. The recording medium according to claim 1, wherein:
the detecting includes subtracting a number of states that are not reached from a total amount of a FSM state coverage, subtracting a number of transitions that do not occur from a total amount of a FSM arc coverage, performing measurement of coverage and calculating a coverage rate, and outputting a result of the calculation.
5. A computer-readable recording medium storing a program for use in FSM coverage measurement based on a language-described logical circuit and a test bench to direct a computer to perform:
extracting a configuration of a FSM from a language description and design information generated based on the language description;
extracting a derivative variable in which a FSM register variable of a FSM is used as input;
extracting a state in which the derivative variable is used as a transition destination of a next state;
extracting a state in which the FSM register variable or the derivative variable is used as a transition condition of a FSM; and
displaying a result of at least one of the extracting the derivative variable in which the FSM register variable of the FSM is used as input and the extracting the state in which the FSM register variable or the derivative variable is used as the transition condition of the FSM.
6. The recording medium according to claim 5, wherein:
the displayed result is an arithmetic result detected by the extracting the derivative variable in which the FSM register variable of the FSM is used as input.
7. The recording medium according to claim 5, wherein:
the displayed result is an arithmetic result detected by the extracting the state in which the FSM register variable or the derivative variable is used as the transition condition of the FSM.
8. A designing apparatus which performs FSM coverage measurement based on a language-described logical circuit and a test bench, comprising:
a FSM check unit to extract a FSM configuration from a language description and design information generated based on the language description, expand hierarchical levels of modules in a range of performing trace back from a variable as input of a FSM to output of a flip-flop or external input of a top module, perform constant propagation and optimization, check before executing a simulation whether or not there is a state that is not reached or a transition that does not occur, and output the check result; and
a FSM coverage measurement unit to subtract the state that is not reached from a total amount of a FSM state coverage, substract the transition that does not occur from a total amount of a FSM arc coverage, perform the FSM coverage measurement based on the test bench, and output a FSM coverage result.
9. The apparatus according to claim 8, wherein:
the FSM check unit is also to extract a derivative variable in which a FSM register variable of the FSM is used as input, a state in which the derivative variable is used as a transition destination of the next state and a state in which the FSM register variable or the derivative variable is used as a transition condition of the FSM.
10. The apparatus according to claim 9, wherein:
an arithmetic result based on the state in which the derivative variable is used as a transition destination of the next state detected by the FSM check unit is displayed.
11. The apparatus according to claim 9, wherein:
an arithmetic result based on the state in which the FSM register variable or the derivative variable is used as a transition condition of the FSM detected by the FSM check unit is displayed.
12. The apparatus according to claim 8, wherein:
the FSM check unit detects by constant propagation whether or not there is a state that is not reached or a transition that does not occur according to an arithmetic result based on a constant propagation logic detected in a FSM input logic and a FSM transition logic.
13. The apparatus according to claim 8, wherein:
the FSM check unit detects whether or not there is a state that is not reached or a transition that does not occur according to an arithmetic result based on exclusive logic detected in the optimized FSM input logic and the FSM transition logic.
14. The apparatus according to claim 8, wherein:
an output of the FSM check unit is a result of subtracting a number of states that are not reached from the total amount of the FSM state coverage, subtracting a number of transitions that do not occur from a total amount of the FSM arc coverage, performing a coverage measurement and calculating a coverage rate.