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The GEMS Launcher main menu provides access to all GEMS Launcher tasks available. The tasks are divided in the following groups:
To start a task, select the appropriate check box and press the button
below the task list.
| Pattern Search & Analysis | ||
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| TF binding sites |
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| Complex Patterns |
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Search for transcription factor binding sites within your
own sequences or sequence databases. GEMS Launcher
comes with a large library
of weight matrix descriptions for transcription factor binding sites
(groups: fungi, insects, plants, miscellaneous, vertebrates, and general
core promoter elements). A IUPAC
library of plant transcription factor binding sites (based on PLACE)
is also included.
The transcription factor binding site matches found by MatInspector are
shown in a table and displayed graphically.
You can search for any IUPAC string in your own sequences or in any of the available sequence databases. This task may be useful if you have a IUPAC description of a transcription factor binding site for which no matrix is available in our library or if you want to check how often a short sequence string occurs in a sequence database.
Graphical display of transcription factor binding sites common to a set of sequences. The common sites are displayed using the Genomatix Java Graphics component, where the matches can be filtered by different criteria.
The input sequences are aligned with DiAlign and transcription factor binding site matches (identified by MatInspector) are displayed within the alignment. It is possible to display all TF binding site matches, common TF binding site matches, or common TF binding site matches that are located in aligned regions.
Automatically scan a set of DNA sequences for orientation and distance correlated transcription factor binding sites. Biological background: polymerase II promoters usually consist of multiple binding sites for transcription factors which mediate the promoter function. However, the specificity of a promoter is not based on single, isolated transcription factor binding sites but rather lies in a defined orientation and distance correlated organization (framework) of a series of those sites. FrameWorker is able to find such conserved organizational patterns. Typical input data sets may be, for instance, a set of promoters from orthologous genes or a set of promoters from different genes which have been found to be co-regulated by cluster analysis of expression array data.
Search for pre-defined promoter modules or user-defined models within your sequences or sequence databases. GEMS Launcher comes with a proven and highly specific library of pre-defined promoter modules. A module is described as two or more transcription factor binding sites in a functionally defined distance range. An example would be a composite element of two transcription factor binding sites acting synergistically as functional subunit of a promoter.
This task allows to search for transcription factor binding site models that are conserved in orthologous promoter sequences of several vertebrate species. This way further evidence for the functionality of promoter models can be gained because TF models are more likely to be functional when they have been preserved during evolution.
Search your sequences for repetitive elements. GEMS Launcher comes with a library of highly specific models for genomic repeats like ALUs or L1-elements which are the most abundant repeats in human genomic sequences. Specific masking of genomic repeats before sequence analysis may reduce false positive results.
GEMS Launcher comes with a highly specific library of retroviral LTR (Long Terminal Repeat) model descriptions to scan your sequences. The library includes models for Lentivirus LTRs, Avian C-type LTRs, and Mammalian C-type LTRs.
This task checks whether a SNP (Single Nucleotide Polymorphism) in your own sequence has any effects on transcription factor binding sites (TF binding sites that are lost or created due to the SNP).
PromoterInspector predicts eukaryotic pol II promoter regions with high specificity in mammalian genomic sequences. PromoterInspector is able to predict promoter regions but not the transcription start site of a gene. The promoter regions predicted might contain the promoter or overlap with the promoter.
Scan your sequences for S/MARs (Scaffold/Matrix Attachment Regions). The program SMARTest predicts potential S/MARs of the AT-rich class in DNA sequences.
Search for restriction sites within your sequences. GEMS Launcher comes with a comprehensive library of sites of restriction enzymes divided in the following groups: 4-cutters, 5-cutters, 6-cutters, 7+-cutters, blunt ends, 3' overhang, and 5' overhang.
| Pattern Definition | ||
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| TF binding sites |
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| Complex Patterns |
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| Experimental Design |
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Fully automatic definition and evaluation of weight matrices from a set of short DNA sequences. The resulting weight matrix can be used in the GEMS Launcher task "MatInspector: Search for transcription factor binding sites" to scan DNA sequences for matches to the defined patterns.
CoreSearch is able to define new motifs that are common to a set of DNA sequences. The motifs found are compared with the MatInspector weight matrix library to check whether the motif is similar to an already known TF binding site. The motifs can be saved as nucleotide weight matrix in your personal matrix library so that they can be used for scanning other sequences with MatInspector.
Automatically scan a set of DNA sequences for orientation and distance correlated transcription factor binding sites. Biological background: polymerase II promoters usually consist of multiple binding sites for transcription factors which mediate the promoter function. However, the specificity of a promoter is not based on single, isolated transcription factor binding sites but rather lies in a defined orientation and distance correlated organization (framework) of a series of those sites. FrameWorker is able to find such conserved organizational patterns. Typical input data sets may be, for instance, a set of promoters from orthologous genes or a set of promoters from different genes which have been found to be co-regulated by cluster analysis of expression array data.
A model describes the occurrence of two or more transcription
factor binding sites (or structural elements of the DNA) in a defined orientation
and distance range. An example would be a promoter model of transcription
factor binding sites that act synergistically. Models can include up
to 10 elements of different types (matrices, IUPACs, direct and
inverted repeats, hairpins).
The models defined can be used in the task
"ModelInspector: Search for promoter modules" to scan DNA
sequences of unlimited length.
This tasks allows you to create primer pairs for one or more sequences according to specifications like length, melting point, etc.
You can perform an in silico design of DNA sequences by selected point mutations. Mutation design of regulatory DNA sequences like promoters or enhancers requires comprehensive knowledge of existence and distribution of potentially functional elements. You can specifically insert or delete certain transcription factor binding sites in a DNA sequence by specific point mutations. SequenceShaper performs an exhaustive check to exclude side effects like unintended insertion or deletion of other transcription factor binding sites and comes up with an optimized mutation design.
| Alignment & Mapping | ||
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Perform a true local multiple alignment. DiAlign is a novel multiple alignment tool using a proprietary algorithm (not based on Needleman-Wunsch algorithm including the Smith-Waterman local variant). DiAlign is based on segment comparison and uses no gap penalty thus avoiding several problems of conventional alignments. One of the most important features of DiAlign is its independence of sequence length in a wide range allowing detection of conserved short stretches directly from a multiple alignment of longer sequences.
The input sequences are aligned with DiAlign and transcription factor binding site matches (identified by MatInspector) are displayed within the alignment. It is possible to display all TF binding site matches, common TF binding site matches, or common TF binding site matches that are located in aligned regions.
Fully automatic mapping of cDNA/mRNA sequences to genomic sequences by ExonMapper. Using this task you can precisely define the exon/intron boundaries of a gene. You need two (sets of) sequences as input, the cDNA/mRNA sequence(s) and the corresponding genomic sequence(s).
Fully automatic mapping of cDNA (mRNA) sequences to genomic sequences in a database. Using this task you can precisely define the exon/intron boundaries of a gene. Submit your (set of) cDNA (mRNA) sequence(s) and a database section as input. GEMS Launcher scans the database for genomic sequence(s) matching the cDNA (mRNA) and subsequently performs the exon/intron mapping.
| Genomatix tools | ||
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| Sequence Tools |
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| Others |
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| Example: | Input sequence: | ACTTGAGGCATTTATACC |
| Reverse-complement: | GGTATAAATGCCTCAAGT |
| Example: | Input sequence: | ACTTGAGGCATTTATACC |
| Extracted: | GAGGCATTTA |
Extract sequences from databases by (a list of) accession numbers, e.g. U01317, Z13985. The extracted sequences can be saved in different sequence formats to your local hard disk and used as data set for subsequent GEMS Launcher analyses.
Reformat your DNA sequences from one format (e.g. GenBank) into another format (e.g. FASTA). Supported sequence formats are: IG, FASTA, GenBank, and EMBL.
The following statistics can be created for your sequences:
GeneRanker allows to characterize gene groups by calculation of p-values for Gene Ontology terms, tissues, dieseases, and signal transduction pathways.
Compare two lists of elements (e.g. sequence names or accession numbers). The result shows the union and the intersection of the two lists as well as the elements that are in only one of the two lists.
Note: Matrix or model library changes (e.g. editing of user-defined matrices or models) are available from the Navigation Bar (see "Projects & Account: "Personal Matrix Library & Subsets" and "Personal Model Library").
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