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Software products developed and distributed by in silico biology, inc.
IMC's workbench consists of the following elements.
Elements marked with * can be docked out (removed) and docked in (incorporated) from the workbench window.
Default feature key
Create, edit, delete feature keys
Feature key search
Attributes of Feature Keys
The feature key that IMC set its own.
There is also a function to remove all of these feature keys at once.
Types and Roles of Qualifiers are explained here.
It collects information on the display method and editing method of Qualifier showing the attribute of Feature.
The following shows two ways of displaying the value of Qualfier described in Feature.
Explanation on the location of the feature on the genome sequence.
Fragmentation of features by restriction enzymes and PCR amplification.
Explain synthesis of features by PCR or ligation.
Feature Fusion is a feature that merges features belonging to the same Feature Key in two identical positions into one. Qualifiers recorded in each feature to be merged are kept equal on either side as the Qualifier of the merged feature.
This feature makes it easy to combine multiple annotations separately attached to the same feature into one.
The Feature operators are logical arithmetic functions of performing logical operations on two mutually overlapping features belonging to the same Feature Key and generating new features.
A feature whose top and bottom overlap, and whose center is computed and generated feature.
About files linked to individual features and how to reference them
Mapping to Individual Features
You can add sequential numbers to features.
Specifically, it is an editing operation that adds a sequential number to one of the qualifiers of the features to which serial numbers are to be added.
You can freely select qualifiers that give target features or serial numbers.
There is also a function to assign sequential numbers across multiple array files.
In addition, it is possible to add serial numbers to features narrowed down as a result of search.
Genome feature map creation / drawing function
By using the feature layout style, you can easily draw feature maps with complicated feature layouts by applying pre-registered layouts when drawing a feature map by combining multiple functional lanes.
In the sequence lane, the base of the currently loaded genome sequence file and the amino acid sequence if it is the coding region are displayed for each strand.
A sequence lane can be placed anywhere in the feature map. You can place more than one sequence lane on one feature map if necessary.
Four bases and 20 amino acids can be displayed individually in different colors.
Changing the drawing color and font size is done in the Sequence Lane tab pane of feature setting dialog.
You can change which position of amino acid 1 character code is placed in codon.
You can not change the font type.
Navigation Lane displays the bird's-eye view map of the entire Feature Map, and you can move the display position of the Feature Map with the slider.
Expression Profile Lane is a lane displaying gene expression profile. (Implemented in Array Edition)
Vertical Scroll Bar Lane
Sequence Scale Lane and Map Scale Lane
This is an operation explanation about the sequence data file, feature data file, optional data file, etc. used in IMC.
Load genomic sequence and amino acid sequence file into IMC.
Save genomic sequence and amino acid sequence as file.
Import data from the outside and map it on the sequence.
Extract data from the sequence and export it externally.
Convert data from one format to another.
Describe operations of restriction enzyme data file, primer data file, option data · file, etc.
Counts the number of feature keys registered in the main current array and displays a list.
Several features to be searched can be selected, and the search range can be limited.
On the search result screen, buttons for feature key number, position on array, base length, gene name, base sequence, button to annotation to descriptions are listed.
In CDS, it is possible to perform operations such as selection of amino acid sequence, + chain strand only, collective deletion, codon table, serial number addition, Fusion PCR.
When you click a line, the main feature map shows the location of that feature.
File output in CSV / FastA / GenBank format is possible.
By simply loading the genomic base sequence into the reference genome map, a database for Blast search is automatically created and homology search (Blast) search for that database can be easily performed.
For homology search, it is necessary to specify the query sequence and sequence database and search program.
Homology search is performed in bacth and mass with all the features present in the designated genomic region as query sequences.
IMC has various display windows as follows.
The description window is a window for entering and editing values in the feature's Qualifier.
It is launched with a right click on the feature and you can edit all the Qualifiers for that feature.
You can also change the Position of the feature.
In addition, you can change the Feature Key to which the feature belongs.
This is a viewer that displays profiles such as secondary structure of amino acid sequence in parallel. Total profile design and display, motif display and so on are possible.
IMC is characterized by being able to perform operations of cloning experiment on computer. At this time, special data is unnecessary, it is possible to clone base sequence data that can be obtained from a public database such as GenBank or EMBL as it is. For cloning, restriction enzyme digestion, PCR primer design, PCR amplification, and ligation can be performed without changing the annotated sequence. All resulting cloning products are output in GenBank / EMBL format. Since Primer information is pasted and stored on the base sequence, it is also useful for Primer management.
IMC has various PCR Primer design methods.
The ability to simply drag the nucleotide sequence on the sequence lane and register it as a primer
Ability to design features on the feature lane and primers to amplify inside and outside the selected area
A function of designing primers that amplify a large number of areas at once (with Iterate Design function: it is a function to repeat the design until there is no area that can not be designed)
The following is a function to design a group of primers for cloning multiple DNA fragments at once, such as gene cluster design. From design to cloning, you can load cloned products into the IMC.
Purpose and overview
Genome annotation is to add an annotation to the genome, more specifically, to describe the attribute (Qualifier) of the feature identified on the genome sequence.
Feature type is classified as Feature Key. The position of Feature is recorded as Position. By the Position on the genome base sequence, the nucleotide sequence occupied by the Feature can be found. In addition, coding region (CDS) translated into amino acid indirectly holds translated amino acid sequence information via Genetic Code Table. It is also important that features such as CDS are identified on either side of the double helix, and it is usually written using the position operator Complement.
Function to draw the feature and the composition of more than one related species genome in parallel on the concentric-circle.
The addendum - the manipulation - a circular lane can be freely deleted from the drawing DIALOG.
It is the designation only of the designation feature content imaging order alteration GenomeMap designation assignment feature in the content skew of the judgement of the chromosome base-sequence of more than one designation in the feature of the judgement of the chromosome base-sequence with more than one annotation.
Independent color setting by the concentric-circle.
Implemented Editions:IMCGE and IMCAE.
This function is installed in the following software
Venn Diagram is a diagram used in set theory, showing the distribution of the number of elements between 3 sets (4 or more sets can be drawn, but IMC draws only 3 sets or less) It is.
Elements belonging to each set are shown in the circle, and overlapping parts are shown as common elements.
It is used for biological applications to illustrate the number of orthologous or unique genes between closely related genomes.
Gene cluster alignment focuses on one gene of a plurality of closely related genomes, and includes the vicinity thereof (N gene ranges in the upstream and N gene ranges in the downstream), and the relationship between the closely related species genome
The presence or absence of homology is investigated, and when there is BBH, homologous genes are combined and displayed in bands.
On the design of gene composition for recombination into heterologous host
Composition automatic design
On the design of gene level
It is a function to check if the gene cluster is designed correctly.
Description of Windows and Dialogs.
Information on large-scale sequencing by NGS and sequencing by conventional capillary sequencer.
Data analysis of NGS can be executed with GenomeTraveler.
Capillary sequencing Data analysis can be performed with IMC.
The lead sequences from the sequencer are linked to each other using homology to generate a consensus sequence.
There are large lead assembly from NGS and assembly from capillary sequencer.
Assembly of NGS leads can be done in GenomeTraveler.
The lead assembly from the capillary sequencer can be executed with the IMC tool in silico Assembler.
We will control the quality of the lead from the sequencer.
We will trim out areas that are not accurate, eliminate leads that are totally inaccurate, and improve assembly accuracy.
IMC has such interesting functions.
Forum in silico, operated by in silico biology inc. provides places for questions, opinions, requests, discussions on products.
Do It Yourself functions for biology.
We have various functions that anyone can design and build genomes.
Tools for genome analysis by your self.
Tools and data available for high school students interested in molecular biology.
To what extent is knowledge necessary to use these tools and data as a whole?
Do It Yourself Biology, definition, conditions, elements, requirements, tools