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| | MAST - Output |
 | | The p-value of a match of a given position within a sequence to a motif is defined as the probability of a randomly selected position in a randomly generated sequence having a match score at least as large as that of the given position. | | | Motif occurrences are determined based on the position p-value of matches to the motif. | | | The p-value of a match of a sequence to a motif is defined as the probability of a randomly generated sequence of the same length having a match score at least as large as the largest match score of any position in the sequence. |
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http://meme.sdsc.edu/meme/website/mast-output.html
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| | [No title] |
| | These variables are based both on the observed characteristics of the sequence being processed and the apriori data input by the user. | | | Functionally, this means that if Gibbs finds it likely that a motif is present more times than the apriori frequency, it is likely to disregard the number input by the user and report a number it finds to match the data more accurately. | | | EM, on the other hand, considers all possibilities at each point using a weighted average system, causing it to use more computing power as more motifs are added to the search. |
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http://users.wpi.edu/~bioinfo/Promoters3-MQP/gibbsintro03.doc
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| | profile.txt |
| | In the first case, the motif search problem is simple and can be solved by a standard optimal alignment algorithm such as described in [1]. | | | As an instruction to software, this parameter means that sequence residues matching profile positions before the `begin' posi- tion should not be reported as being part of the biological object. | | | The designa- tion `quantitative' means that a motif description assigns a degree of similarity to a potential match rather than a binary status of true or false. |
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http://www.expasy.ch/txt/profile.txt
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| | MAST |
| | The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entry from each column of the position-dependent scoring matrix that represents the motif. | | | The positions and p-values of the non-overlapping motif occurrences are shown above the actual sequence for each of the high-scoring sequences from Section I. A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001 as defined in Section II. | | | The ordering and spacing of all non-overlapping motif occurrences are shown for each high-scoring sequence listed in Section I. A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001. |
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http://users.wpi.edu/~bioinfo/Promoters3-MQP/mast.CBSeamCell.meme.html
(678 words)
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| | Current Protocols in Bioinformatics: MEME |
| | MEME looks for the most "significant" motifs in the input sequences, where "significant" is a function of the length of the pattern, number of times it occurs and degree of similarity among the occurrences. | | | For a motif to be useful for database searches, it must as a rule contain at least log_2(N) bits of information where N is the number of sequences in the database being searched. | | | The matching motifs occur in the same order as the training set sequences, except for a second match to motif 1 in the second sequence where motif 5 would be expected. |
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http://www.sdsc.edu/~tbailey/MEME-protocol-draft2/protocols.html
(6639 words)
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| | Sequence motif - Wikipedia, the free encyclopedia |
| | There are software programs which, given multiple input sequences, attempt to identify one or more candidate motifs. | | | The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: | | | Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. |
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http://en.wikipedia.org/wiki/Sequence_motif
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| | Scansite Menu |
| | A problem that caused an internal server error on some input sequences was fixed. | | | Batch versions of the Motif Scan programs are now available using the program "Scan Many Proteins Simultaneously". | | | In the Motif Scan program, choose a Swiss-Prot ID/Accession and submit. |
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http://scansite.mit.edu
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| | [No title] |
| | /* MOTIF This program looks for a sequence motif defined by the user in the sequence(s) contained in the database file specified. | | | DEFAULT: VERBOSE"); printf("\n\n"); printf(" BRIEF : only the number of matches in a sequence are report.\n"); printf(" COMPACT: number and positions of matches are reported.\n"); printf(" VERBOSE: number, positions and sequences of matches"); printf(" are reported.\n"); exit(0); } | | | 0)) { if (matches > 1) fprintf(rfil,"\n"); fprintf(rfil,"match at %d, sequence matched: ",i+1); for (k=i;k |
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http://ftp.sunet.se/pub/molbio/pattern/motif.c
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| | The Scientist - Web BioSphere |
| | Protein Motif Analysis - Compare a query sequence against PROSITE - IBCP (France) | | | FASTA-PAT - Search of a Pattern Database with a Query Protein Sequence - BCM (US) | | | SeqhuntII - Search of Kabat Database with a Query Pattern/Motif - NWU (US) |
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http://www.sdsc.edu/~csmith/bioweb/pmotif.html
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| | How can make a motif into a regular expression? |
| | The generated Pattern can even be from an ambiguous sequence such as "acgytnwacrs" | | | * The motif can contain Ambiguity symbols * Lists the ORF title and position of motif * Outputs a list of counts to stdout. | | | You can then use this Pattern to search Strings for the existance of that Pattern. |
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http://www.biojava.org/docs/bj_in_anger/regex.html
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| | Microsatellite documentation. |
| | Function: get/set the end position of the repeat in this sequence | | | depends on having information for the motif and the number of | | | Returns : A scalar representing the current sequence of this |
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http://doc.bioperl.org/releases/bioperl-1.4/Bio/Map/Microsatellite.html
(535 words)
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| | DNA Sequence & Structural Analyses |
| | Sequence-To-Cluster - Align Query Sequence aginst PIMA Multiple Alignment/Pattern - BCM (US) | | | GenQuest - Query Nucleotide/Protein Sequence Comparison against Nucleotide/Protein Sequence Databases - ORNL (US) | | | RepEater - Search for Sequence Repeats in Query Sequence - Weisman Institute (Israel) |
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http://restools.sdsc.edu/biotools/biotools16.html
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| | Further Improvements on SMART: (ResearchIndex) |
| | Abstract: We present further improvements on the computer system SMART (sequence motif analysis and retrieval tool) that assists biological interpretation of sequence data by searching sequence motifs in a query sequence and annotating functional features associated with the motifs found. | | | The new version of the system fully utilizes the network communication based on a client-server model so that users run only the client program on their workstations without any database resources locally. | | | Sequence Motif Analysis and Retrieval Tool A. Ogiwara I. Uchiyama... |
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http://citeseer.ist.psu.edu/603520.html
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| | Upstream Sequence Motif Analysis of Human Ig and TCR Genes |
| | An analysis of upstream sequences (-1000 to + 10) from 356 human Ig and 242 human TCR genes employing the Gibbs Motif Sampler (http://www.bioinfo.rpi.edu/applications/bayesian/gibbs/gibbs.html) and MEME (http://meme.sdsc.edu) software was performed. | | | The biological relevance of these findings with respect to sterile transcription and germline gene rearrangement in immune cells need to be explored in order to verify the significance of this computational approach in studying transcriptional control mechanisms in this system. | | | An informatic approach to analyze the sterile transcriptional mechanisms of a whole set of human Ig or TCR genes has been developed. |
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http://www.iscb.org/ismb2004/posters/nperumalATiupui.edu_1033.html
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| | Table of microsatellite sequence motif permutations |
| | Appendix A SSR sequence permutations: Sequence motifs are ordered alphabetically in the left column, complementary sequences are to the right of the double bar. |
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http://dendrome.ucdavis.edu/dendrome_genome/cetable.html
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| | MOTIF: Searching Protein and Nucleic Acid Sequence Motifs |
| | The old form is no longer automatically redirected. | | | You may want to update your bookmarks accordingly, or, if you came here from another Web page, inform the maintainer of that page to update their link to us. | | | MOTIF: Searching Protein and Nucleic Acid Sequence Motifs is now: |
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http://motif.genome.ad.jp
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| | The homeobox page |
| | Kappen, C., Schughart, K., Ruddle, F.H. (1993) Early evolutionary origin of major homeodomain sequence classes. | | | However, many homeobox genes are not homeotic genes; the homeobox is a sequence motif, while "homeotic" is a functional description for genes that cause homeotic transformations." | | | The first genes found to encode homeodomain proteins were Drosophila developmental control genes, in particular homeotic genes, from which the name "homeo"box was derived. |
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http://homeobox.biosci.ki.se
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| | GenomeNet |
| | Complete Genomes in KEGG (Last updated: June 1, 2002) | | | DBGET KEGG SSDB LIGAND BRITE BLAST FASTA MOTIF CLUSTALW |
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http://www.jaist.genome.ad.jp
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