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Iccare |  |
| Interspecific Comparative Clustering and Annotation foR Est |  |
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Iccare | |
| Interspecific Comparative Clustering and Annotation foR Est | |
Homepage
The Homepage [See it] presents two kinds of information. The first is instruction and information about the working process of Iccare with the "Documentation & Reference" [See it] and the "Tutorial". The second is the practical result of Iccare for sequence of the query organisms (see next paragraph: taxonomic tree) or with "Your Own Sequence" [See it].
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The taxonmic tree presents some animal and plant phylums. Mouseover on light green (plant) and red (animal) phylum shows the query organisms available for this phylum which can be selected for analysis (bring to the "Organism Selection", See it). Dark green (plant) and mauve (animal) phylums are not available now.
Your Own Sequence Search
On the "Your Own sequence Search" page [See it], you can launch a BLAST of your own sequence(s) against all human or arabidopsis transcripts. The results are displayed on the same scheme that for the query organisms.
Submission proceed :
For more information, click on the readmefirst to visualize one example of plant or animal results.
- Paste one or more sequence in fasta (or browse a fasta file).
- Select one model organism (on the right).
- Enter your e-mail. Necessary !!
- Press the blast buttom.
Iccare computes information and informs you by e-mail that the results are available. You can access your results via the result page following your request or with the URL given into the e-mail. The result page [See it] permits to visualize 3 information. The first is the distribution of all genes of the model organism which present similitudes with your sequences on the karyotype of the model organism ("Comparative Mapping (Karyotype)", see it). The second permits to verify your sequence by clicking on its name. And the last permits to visualize one gene of the model organism which present similitudes with one of your sequence ("Comparative Mapping (Chromosome)" see it).
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To visualize the alignment between your sequence and the gene of the model organism, design primers or overgo probes, go to the paragraph Comparative Mapping (Chromosome), the Description Page, the Gene Structure Representation, the Local or Global Alignment Representation.
Documentation & Reference
The Documentation & Reference page [See it] contains all information about the material and methods, the resources, the database (NCBI, MIPS, Ensembl or Infobiogen) and at least the publication references used on Iccare.
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Organism Selection
The "Organism Selection" page [See it] permits to select a query organism belonging to the selected phylum. Only organism in blue can be selected and bring to the "Comparative Mapping (Karyotype)" [See it]. If this organism belongs to plant kingdom, it will be compared to Arabidopsis thaliana if not it will be compared to Homo sapiens.
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Comparative Mapping (karyotype)
The "Comparative Mapping (karyotype)" page [See it] gives information about the distribution of gene on the karyotype of the model organism. The green genes present similarities with ESTs of the query organism or with your personal sequences ; the blue ones are genes of the model organism without similarity.
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From this page, you can access to the "Older versions" [See it] of Iccare process for this query organism. In addition, the footer page contains two search tools. The first permits to find a particular gene of the model organism with is Identifier which bring to the Comparative Mapping (Chromosome) [for example : gene CRYBB3, See it]. The second allows to find an EST of the query organism with its GenBank Identifier or to find a personal sequence with its Identifier which bring to the Description Page [for example : EST BG383527, See it].
Older Versions
The "Older Versions" page [See it] allows to visualize the comparison results of an older UniGene or MIPS data version of the model organism and an older version of query sequence data. You have to select a version for the selected query organism which brings to the "Comparative Mapping (Karyotype)" [See it]. If this organism belongs to plant kingdom, it will be compared to Arabidopsis thaliana if not it will be compared to Homo sapiens.
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Comparative Mapping (chromosome)
The "Comparative Mapping (chromosome)" page [See it] gives information about the distribution of gene on one chromosome of the model organism. The green genes present similarities with ESTs of the query organism or with your personal sequences ; the blue ones are genes of the model organism without similarity.
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From this page, you can access to the caption [See it] and return on the "Comparative Mapping (karytoype)" [See it]. Mouseover on gene name shows an Information box containing the gene name, its position in Megabase, the cytogenetic band name, the query organism name which is a dynamic link to the "Description Page" [See it] and the number of sequences with similarity for this gene.
In addition, options can be selected to navigate on the image (the "move up/down" buttons), to enlarge or reduce in size ("zoom in/out" buttons), to select a particular chromosome region ("go to" button), to view the orthology relationship between human and mouse sequence ("known orthology" button) and to find a particular gene ("look up" button).
Description Page
The "Description Page" [See it] contains the Iccare version, a caption (french and english, See it), information about the gene of the model organism (name, putative function, chromosome number and position, etc...), "Alignment" linked to the Gene Structure Representation [See it] and a table containing information about the query organism sequences or personal sequence presenting similarities with gene of the model organism. You can also find a BLAST search link, blastn and tblastx, in order to view the BLAST results of one query organism sequence or one personal sequence against all the genes of the model organism [blastn, See it ; tblastx, See it].
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Gene Structure Representation
The "Gene Structure Representation" page [See it] contains the representation of the gene structure of the model organism and the similitudes representation between the gene of the model organism and the sequences of the query organism or your personal sequence(s).
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The first rectangle contains genomic information for the gene of the model organism :
The first line is the genomic representation ; the genomic DNA symbolized by the horizontal black line, the ordinate in bases placed above or under the black line (gives the gene position on the chromosome), green or yellow boxes and the number associated represent exons and the numbers placed between the exons are the intron sizes. The second line represents the structure of the mRNA (exon/intron) ; the ordinate in bases symbolized by the black line and the alternative blue and mauve numbered boxes are the exons. The last line represents the translated region of the mRNA ; the RNA symbolized by the black line, the ordinate in bases placed under and the translated region symbolized by the blue box.
The second rectangle is the representation of the query sequences or personal sequence presenting similarities with the gene of the model organism :
On the right part, EST sequence information (GenBank Identifier, sequence size, BLASTN e-value) is placed and on the left part is the sequence representation. The black line symbolizes the EST sequence, an ordinate in bases is placed under, green boxes correspond to sequence similarities with the gene of the model organism on the same strand while yellow boxes correspond to similarities in a reverse-complement manner. Each box is linked to the "Local Alignment Representation" [See it].
Under the rectangles, sequences similarities with additional query species are also available ("+" buttons). The Global (Needleman-Wunsch software) or the Local (Smith-Waterman software) Alignment is available. you can compare one gene of the model organism and one query organism sequences / one personal sequence or two query sequences (link to "Local or Global Alignment Representation").
Local or Global Alignment Representation
The "Local or Global Alignment Representation" page [See it] contains the display associated to the result of a local alignement between the gene of the model organism and the sequence of the query organism or your personal sequence. BLASTN information (score, expect, identities, gaps and strand) is placed on the top. The query nucleic sequence is represented in black and the nucleic sequence of the model organism is represented in alternative blue and mauve letters corresponding to the different exons. Moreover, under the sequence of the model organism is placed a simple pattern repeat of dash and point "--.--.--." ; Each pattern "--." corresponds to one codon and the point indicate the third base of the codon. Genomic sequences without pattern under correspond to untranslated sequences.
Three tools are placed on the foot page:return to index
- Primer design:
To design efficient primers to detect polymorphism, you can design primers on exons surrounding one intron [See it].
- Translated sequence:
To visualize the translated sequence, you have to indicate the start base to operate the translation, for example on base 63 (first Open Reading Frame) [See it] or on base 65 (third ORF) [See it]. Translate the sequence in the right ORF gives the animo acid sequence and permits to visualize the polymorphism existing between the two protein sequences. Translate the sequence in the third ORF gives the polymorphism information related to the third codon base of the nucleic sequence not visualizable with the translation on the first ORF.
- Overgo maker:
To design efficient overgo probes, design your overgo on conserved exon. Give the start and the end position of the exon, for example exon number 4 (base 257 to 389) [See it].
Iccare web site Architecture
Green arrows indicate all the link to information, caption or tutorial in order to better understand the Iccare Web server.
The description paragraph is accessible by clicking on rectangle of the image.
Red arrows indicate pathway to access the result of query organism sequences.
Blue arrows indicate the pathway of your personal sequence submission.
Pink arrows indicate the tool available on Iccare to work on the EST sequences.
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FAQ :
How to select an EST of the query organism presenting similarity with one Arabidopsis or Human gene ? First, you have to select on the Iccare "Homepage" [See it] one phylum (containing the query organism of interest) on the taxonomic tree. Now, you are on the "Organism Selection" page [See it] and you have to select one query organism. The "Comparative mapping (Karyotype)" page [See it] is opened and you have several possibilities to select an EST of the query organism presenting similarity with one Arabidopsis or human gene:
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- if you search for a particular EST:
On the foot page, enter the EST ID and launch the search, for example the EST BG383527 of Sus scrofa. If the EST presents similarity with one gene of the model organism, the "Description Page" is returned [See it], if not, the result page returned contains the following message: There are no answers to the request.
- if you search for a particular Arabidopsis or human gene:
On the foot page, enter the gene ID and launch the search, for example the human gene CRYBB3. The result [See it] is presenting on the "Comparative mapping (Chromosome)" page and an arrow indicates the location of the gene on the chromosome of the model organism. If the gene presents similarity with one or more EST of the query organism the gene is written in green, if not, the gene is written in black.
- if you search for a particular chromosomic region:
First select one chromosome. The "Comparative mapping (Chromosome)" page gives the chromosome scale representation [See it]. Green rectangles (green gene name) near the chromosome representation present the gene with similarity and blue ones (black gene name) are those without. Use the "Go to" button to select a particular region, for example the 21-26 Mbase region. The results [See it] are presenting in a higher resolution, but if the resolution is not sufficient, use the "zoom in" button to enlarge the representation. Now you can select any green gene of the model organism.
How to compare my own sequence(s) to Arabidopsis or Human gene ? First, you have to select on the Iccare "Homepage" [See it] the "Your Own sequence Search" on the tool bar. On this page [See it], paste one or more sequence in fasta (or browse a fasta file). Next, select one model organism (on the right) and enter your e-mail (Necessary !!). Now press the blast buttom.
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Iccare computes information and informs you by e-mail that the results are available. You can access your results via the result page following your request or with the URL given into the e-mail.
How to predict the exon splicing of one EST from the Arabidopsis or Human gene structure ? Having select an EST (see the "How to select an EST of the query organism presenting similarity with one Arabidopsis or Human gene ?") gives access to the "Description Page", for example the EST BG383527 of Sus scrofa [See it]. On this page, the "Alignment" link permits to vizualise the "Gene Structure Representation" [See it]. The first rectangle gives the genomic structure of the gene of the model organism. The second rectangle gives information about the sequences of the query organism which are symbolized by a black line and yellow or green rectangles are the region presenting similarities with the gene of the model organism. Each rectangle are linked to the "Local Alignment Representation". This page [See it] contains the display associated to the result of a local alignement between the gene of the model organism and the sequence of the query organism or your personal sequence. The query nucleic sequence is represented in black and the nucleic sequence of the model organism is represented in alternative blue and mauve letters corresponding to the different exons. With this information, you can transpose the splicing site from the model organism to the query organism and specifically amplify introns by designing primers in exons surrounding or overgo probes on conserved exons.
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How to translate an EST and compare it to the translated Arabidopsis or Human gene ? Having select an EST and accessing the "Gene Struture Representation" (see the "How to predict the exon splicing of one EST from the Arabidopsis or Human gene structure ?") gives access to the "Local Alignment Representation", for example the EST BG383527 of Sus scrofa. This page [See it], contains the display associated to the result of a local alignement between the gene of the model organism and the sequence of the query organism or your personal sequence. The query nucleic sequence is represented in black and the nucleic sequence of the model organism is represented in alternative blue and mauve letters corresponding to the different exons. Under the sequence of the model organism is placed a simple pattern repeat of dash and point "--.--.--." ; Each pattern "--." corresponds to one codon and the point indicate the third base of the codon. To vizualize the translated region of the gene of the model organism, give the start codon to operate the translation. Now, you can indicate where you want to start the translation, for example on base 63 (first Open Reading Frame) [See it] or on base 65 (third ORF) [See it].
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How to design efficient primer or overgo probes from an EST ? Having select an EST and accessing the "Gene Struture Representation" (see the "How to predict the exon splicing of one EST from the Arabidopsis or Human gene structure ?") gives access to the "Local Alignment Representation", for example the EST BG383527 of Sus scrofa. This page [See it], contains the display associated to the result of a local alignement between the gene of the model organism and the sequence of the query organism or your personal sequence. The query nucleic sequence is represented in black and the nucleic sequence of the model organism is represented in alternative blue and mauve letters corresponding to the different exons.
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- To design primers to search polymorphism:
Use exons surrounding one intron and design primers on these exons, for example design primers to amplify the intron number 3 in region 138-389 base [See it].
- To design overgos:
Use conserved exons and avoid the splicing region, for example design overgo in exon number 4 region 257-389 base [See it].
For any questions or comments please contact us : Iccare
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© Iccare : Laboratoire de génétique cellulaire - INRA &
Laboratoire de Biotechnologies et d'Amélioration des Plantes - INP-ENSAT.
Created by Faraut & Muller 02/2003 .