HMMBuildDialog ... ... HMM Build HMM Build Multiple alignment file: Multiple alignment file: File to save HMM profile: File to save HMM profile: Expert options Expert options Name can be any string of non-whitespace characters (e.g. one ”word”). Name can be any string of non-whitespace characters (e.g. one ”word”). Name this HMM: Name this HMM: By default, the model is configured to find one or more nonoverlapping alignments to the complete model: multiple global alignments with respect to the model, and local with respect to the sequence By default, the model is configured to find one or more nonoverlapping alignments to the complete model: multiple global alignments with respect to the model, and local with respect to the sequence Default (hmmls) behaviour: Default (hmmls) behaviour: Configure the model for finding multiple domains per sequence, where each domain can be a local (fragmentary) alignment. This is analogous to the old hmmfs program of HMMER 1. Configure the model for finding multiple domains per sequence, where each domain can be a local (fragmentary) alignment. This is analogous to the old hmmfs program of HMMER 1. Emulate hmmfs behaviour: Emulate hmmfs behaviour: Configure the model for finding a single global alignment to a target sequence, analogous to the old hmms program of HMMER 1. Configure the model for finding a single global alignment to a target sequence, analogous to the old hmms program of HMMER 1. Emulate hmms behaviour: Emulate hmms behaviour: Configure the model for finding a single local alignment per target sequence. This is analogous to the standard Smith/Waterman algorithm or the hmmsw program of HMMER 1. Configure the model for finding a single local alignment per target sequence. This is analogous to the standard Smith/Waterman algorithm or the hmmsw program of HMMER 1. Emulate hmmsw behaviour: Emulate hmmsw behaviour: HMMBuildWorker Fix the length of the random sequences to <n>, where <n> is a positive (and reasonably sized) integer. <p>The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. Fix the length of the random sequences to <n>, where <n> is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. Mean length of the synthetic sequences, positive real number. The default value is 325. Mean length of the synthetic sequences, positive real number. The default value is 325. Number of synthetic sequences. If <n> is less than about 1000, the fit to the EVD may fail. <p>Higher numbers of <n> will give better determined EVD parameters. <p>The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time. Number of synthetic sequences. If <n> is less than about 1000, the fit to the EVD may fail. Higher numbers of <n> will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time. Standard deviation of the synthetic sequence length. A positive number. <p>The default is 200. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0. Standard deviation of the synthetic sequence length. A positive number. <p>The default is 200. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0. The random seed, where <n> is a positive integer. <p>The default is to use time() to generate a different seed for each run, <p>which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. <p>You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM. The random seed, where <n> is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM. HMMCalibrateDialog HMM file: HMM file: ... ... Expert options Expert options Fix the length of the random sequences to n , where n is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. Fix the length of the random sequences to n, where n is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. Fix the length of the random sequences to: Fix the length of the random sequences to: Mean length of the synthetic sequences: Mean length of the synthetic sequences: Number of synthetic sequences. If n is less than about 1000, the fit to the EVD may fail Higher numbers of n will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time. Number of synthetic sequences. If n is less than about 1000, the fit to the EVD may fail Higher numbers of n will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time. Number of synthetic sequences: Number of synthetic sequences: Standard deviation of the synthetic sequence length. A positive number. The default is 200. Note that the Gaussian is left-truncated so that no sequences have lengths less or equal 0. Standard deviation of the synthetic sequence length. A positive number. The default is 200. Note that the Gaussian is left-truncated so that no sequences have lengths less or equal 0. Standard deviation: Standard deviation: The random seed, where n is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM. The random seed, where n is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM. Random seed: Random seed: Save calibrated profile to file Save calibrated profile to file Save calibrated profile to file: Save calibrated profile to file: HMM Calibrate HMM Calibrate Mean length of the synthetic sequences, positive real number. The default value is 325. Mean length of the synthetic sequences, positive real number. The default value is 325. HMMSearchDialog HMM Search HMM Search File with HMM profile: File with HMM profile: ... ... Expert options Expert options E-value filtering can be used to exclude low-probability hits from result. E-value filtering can be used to exclude low-probability hits from result. Filter results with E-value greater then: Filter results with E-value greater then: Score based filtering is an alternative to E-value filtering to exclude low-probability hits from result. Score based filtering is an alternative to E-value filtering to exclude low-probability hits from result. Filter results with Score lower than: Filter results with Score lower than: Calculate the E-value scores as if we had seen a sequence database of <n> sequences. Calculate the E-value scores as if we had seen a sequence database of <n> sequences. Number of sequences in dababase: Number of sequences in dababase: Variants of algorithm Variants of algorithm 1E 1e Algorithm Calculate the E-value scores as if we had seen a sequence database of &lt;n&gt; sequences. Calculate the E-value scores as if we had seen a sequence database of <n> sequences. QObject HMM Profile HMM Profile U2::GTest_uHMMERCalibrate uhmmer-calibrate-subtask HMM Calibrate U2::HMM2QDActor HMM2 HMM2 QD HMM2 search QD HMM2 search Power of e-value must be less or equal to zero. Using default value: 1e-1 Power of e-value must be less or equal to zero. Using default value: 1e-1 Searches HMM signals in a sequence with one or more profile HMM2 and saves the results as annotations. Searches HMM signals in a sequence with one or more profile HMM2 and saves the results as annotations. Profile HMM Profile HMM Semicolon-separated list of input HMM files. Semicolon-separated list of input HMM files. Min Length Min Length Minimum length of a result region. Minimum length of a result region. Max Length Max Length Maximum length of a result region. Maximum length of a result region. Filter by High E-value Filter by High E-value Reports domains &lt;= this E-value threshold in output. Reports domains &lt;= this E-value threshold in output. Filter by Low Score Filter by Low Score Reports domains &gt;= this score cutoff in output. Reports domains &gt;= this score cutoff in output. Number of Sequences Number of Sequences Specifies number of significant sequences. It is used for domain E-value calculations. Specifies number of significant sequences. It is used for domain E-value calculations. U2::HMMADVContext Search with HMM model... Search with HMM model... Find HMM signals with HMMER2... Find HMM signals with HMMER2... Error Error No sequences found No sequences found U2::HMMBuildDialogController Build Build Close Close Select file with alignment Select file with alignment Select file with HMM profile Incorrect alignment file! Incorrect alignment file! Incorrect HMM file! Incorrect HMM file! Error Error Starting build process Starting build process Hide Hide Cancel Cancel HMM build finished with errors: %1 HMM build finished with errors: %1 HMM build canceled HMM build canceled HMM build finished successfuly! HMM build finished successfuly! Progress: %1% Progress: %1% HMM models HMM models U2::HMMBuildTask Build HMM profile '%1' Multiple alignment is empty Multiple alignment is empty Multiple alignment is of 0 length Multiple alignment is of 0 length Invalid alphabet! Only amino and nucleic alphabets are supported Invalid alphabet! Only amino and nucleic alphabets are supported Error creating MSA structure Error creating MSA structure U2::HMMBuildToFileTask none none Build HMM profile '%1' -> '%2' Build HMM profile '%1' -> '%2' Error reading alignment file Error reading alignment file Build HMM profile to '%1' Build HMM profile to '%1' Incorrect input file Incorrect input file Alignment object not found! Alignment object not found! Source alignment Source alignment Profile name Profile name Task was not finished Task was not finished Profile file Profile file Expert options Expert options U2::HMMCalibrateDialogController Calibrate Calibrate Close Close Select file with HMM model Select file with HMM model Incorrect HMM file! Incorrect HMM file! Illegal fixed length value! Illegal fixed length value! Invalid output file name Invalid output file name Error Error Starting calibration process Starting calibration process Hide Hide Cancel Cancel Calibration finished with errors: %1 Calibration finished with errors: %1 Calibration was cancelled Calibration was cancelled Calibration finished successfuly! Calibration finished successfuly! Progress: %1% Progress: %1% HMM models HMM models U2::HMMCalibrateParallelSubTask Parallel HMM calibration subtask Parallel HMM calibration subtask U2::HMMCalibrateParallelTask HMM calibrate '%1' HMM calibrate '%1' U2::HMMCalibrateTask HMM calibrate '%1' HMM calibrate '%1' U2::HMMCalibrateToFileTask HMM calibrate '%1' HMM calibrate '%1' Source profile Source profile Task was not finished Task was not finished Result profile Result profile Expert options Expert options Number of random sequences to sample Number of random sequences to sample Random number seed Random number seed Mean of length distribution Mean of length distribution Standard deviation of length distribution Standard deviation of length distribution Calculated evidence (mu , lambda) Calculated evidence (mu , lambda) U2::HMMCreateWPoolTask Initialize parallel context U2::HMMIO ALPH must precede NULE in HMM save files ALPH must precede NULE in HMM save files Illegal line Illegal line File format is not supported File format is not supported Invalid file structure near %1 Invalid file structure near %1 Value is illegal: %1 Value is illegal: %1 Alphabet is not set Alphabet is not set Value is not set for '%1' Value is not set for '%1' No '//' symbol found No '//' symbol found HMM models HMM models U2::HMMMSAEditorContext Build HMMER2 profile Build HMMER2 profile U2::HMMReadTask Read HMM profile '%1'. Read HMM profile '%1'. U2::HMMSearchDialogController Select file with HMM model Select file with HMM model HMM file not set! HMM file not set! Error Error Cannot create an annotation object. Please check settings Cannot create an annotation object. Please check settings Starting search process Starting search process Hide Hide Cancel Cancel HMM search finished with error: %1 HMM search finished with error: %1 HMM search finished successfuly! HMM search finished successfuly! Progress: %1% Progress: %1% Cell BE optimized Cell BE optimized Search Search Close Close SSE optimized SSE optimized Conservative Conservative U2::HMMSearchTask HMM Search HMM Search Invalid HMM alphabet! Invalid HMM alphabet! Invalid sequence alphabet! Invalid sequence alphabet! Amino translation is not available for the sequence alphabet! Amino translation is not available for the sequence alphabet! Parallel HMM search Parallel HMM search HMM search with '%1' HMM search with '%1' U2::HMMSearchToAnnotationsTask HMM search, file '%1' HMM search, file '%1' RAW alphabet is not supported! RAW alphabet is not supported! Annotation object was removed Annotation object was removed HMM profile used HMM profile used Task was not finished Task was not finished Result annotation table Result annotation table Result annotation group Result annotation group Result annotation name Result annotation name Results count Results count U2::HMMWriteTask Write HMM profile '%1' Write HMM profile '%1' U2::LocalWorkflow::HMMBuildPrompter For each MSA from <u>%1</u>, For each MSA from <u>%1</u>, and calibrate and calibrate default default custom custom %1 build%2 HMM profile using <u>%3</u> settings. %1 build%2 HMM profile using <u>%3</u> settings. U2::LocalWorkflow::HMMBuildWorker Built HMM profile Built HMM profile Calibrated HMM profile Calibrated HMM profile HMM2 Build HMM2 Build HMM profile HMM profile HMM strategy HMM strategy Specifies kind of alignments you want to allow. Specifies kind of alignments you want to allow. Profile name Profile name Descriptive name of the HMM profile. Descriptive name of the HMM profile. Calibrate profile Calibrate profile Parallel calibration Parallel calibration Fixed length of samples Fixed length of samples Mean length of samples Mean length of samples Number of samples Number of samples Standard deviation Standard deviation Random seed Random seed HMM Build HMM Build Default Default Incorrect value for seed parameter Incorrect value for seed parameter Schema name not specified. Using default value: '%1' Schema name not specified. Using default value: '%1' Input MSA Input MSA Input multiple sequence alignment for building statistical model. Input multiple sequence alignment for building statistical model. Produced HMM profile Produced HMM profile Enables/disables optional profile calibration.<p>An empirical HMM calibration costs time but it only has to be done once per model, and can greatly increase the sensitivity of a database search. Enables/disables optional profile calibration.<p>An empirical HMM calibration costs time but it only has to be done once per model, and can greatly increase the sensitivity of a database search. Number of parallel threads that the calibration will run in. Number of parallel threads that the calibration will run in. Builds a HMM profile from a multiple sequence alignment.<p>The HMM profile is a statistical model which captures position-specific information about how conserved each column of the alignment is, and which residues are likely. Builds a HMM profile from a multiple sequence alignment.<p>The HMM profile is a statistical model which captures position-specific information about how conserved each column of the alignment is, and which residues are likely. U2::LocalWorkflow::HMMLib HMM Profile HMM Profile HMM profile HMM profile Location Location Read HMM2 Profile Read HMM2 Profile Write HMM2 Profile Write HMM2 Profile HMMER2 Tools HMMER2 Tools Input HMM profile Input HMM profile Location hint for the target file. Location hint for the target file. Saves all input HMM profiles to specified location. Saves all input HMM profiles to specified location. Reads HMM profiles from file(s). The files can be local or Internet URLs. Reads HMM profiles from file(s). The files can be local or Internet URLs. Loaded HMM profile Loaded HMM profile U2::LocalWorkflow::HMMReadPrompter Read HMM profile(s) from %1. Read HMM profile(s) from %1. U2::LocalWorkflow::HMMReader Loaded HMM profile from %1 Loaded HMM profile from %1 U2::LocalWorkflow::HMMSearchPrompter For each sequence from <u>%1</u>, For each sequence from <u>%1</u>, Use <u>default</u> settings. Use <u>default</u> settings. Use <u>custom</u> settings. Use <u>custom</u> settings. %1 HMM signals%2. %3<br>Output the list of found regions annotated as <u>%4</u>. %1 HMM signals%2. %3<br>Output the list of found regions annotated as <u>%4</u>. using all profiles provided by <u>%1</u>, using all profiles provided by <u>%1</u>, U2::LocalWorkflow::HMMSearchWorker Bad sequence supplied to input: %1 Bad sequence supplied to input: %1 Found %1 HMM signals Found %1 HMM signals HMM profile HMM profile Input sequence Input sequence HMM annotations HMM annotations Result annotation Result annotation Number of seqs Number of seqs Filter by high E-value Filter by high E-value Filter by low score Filter by low score HMM2 Search HMM2 Search Power of e-value must be less or equal to zero. Using default value: 1e-1 Power of e-value must be less or equal to zero. Using default value: 1e-1 Value for attribute name is empty, default name used Value for attribute name is empty, default name used Find HMM signals in %1 Find HMM signals in %1 HMM profile(s) to search with. HMM profile(s) to search with. An input sequence (nucleotide or protein) to search in. An input sequence (nucleotide or protein) to search in. Annotations marking found similar sequence regions. Annotations marking found similar sequence regions. A name of the result annotations. A name of the result annotations. HMM Search HMM Search Searches each input sequence for significantly similar sequence matches to all specified HMM profiles. In case several profiles were supplied, searches with all profiles one by one and outputs united set of annotations for each sequence. Searches each input sequence for significantly similar sequence matches to all specified HMM profiles. In case several profiles were supplied, searches with all profiles one by one and outputs united set of annotations for each sequence. U2::LocalWorkflow::HMMWritePrompter unset unset Save HMM profile(s) from <u>%1</u> to <u>%2</u>. Save HMM profile(s) from <u>%1</u> to <u>%2</u>. U2::LocalWorkflow::HMMWriter Empty HMM passed for writing to %1 Empty HMM passed for writing to %1 Unspecified URL for writing HMM Unspecified URL for writing HMM Writing HMM profile to %1 Writing HMM profile to %1 U2::UHMMBuild bogus configuration choice bogus configuration choice U2::uHMMPlugin HMM2 HMM2 Based on HMMER 2.3.2 package. Biological sequence analysis using profile hidden Markov models Based on HMMER 2.3.2 package. Biological sequence analysis using profile hidden Markov models Build HMM2 profile... Build HMM2 profile... Calibrate profile with HMMER2... Calibrate profile with HMMER2... Search with HMMER2... Search with HMMER2... Error Error Error! Select sequence in Project view or open sequence view. Error! Select sequence in Project view or open sequence view.