eShop in silico

Feature Keys

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

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.

• The above figure is a feature lane of the forward strand in three frame format.
• The following functions can be executed from the feature lane setting dialog.
• Display feature key (s), strand selection, arrangement method (Six Lane, Three Lane, Two Lane, One Lane, Pack), Chain change (Forward, Reverse, Both), Exon display method change, Placement density, Lane Height change, offset change. 

• The items that can be set from the content / profile lane setting dialog are as follows.
• Change the background color, change the parameters of the profile graph, change sliding window parameters, thinning out (6 contents, such as GC Content, GC / AT Skew, Cumulative GC / AT Skew, Import Map Data, Fickett Profile) Function, change graph color.

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.

• The items that can be changed from the navigation lane setting dialog are as follows.
• Feature (s) can be selected. Strand selection (Forward, Reverse, Both), placement method selection (Six Lane, Three Lane, Two Lane, One Lane, Pack), thinning setting change.

• The items that can be changed from the restriction enzyme lane setting dialog are as follows.
• Lane height, set switching, narrowing down of restriction enzyme list (recognition sequence length, palindromicity, terminal shape (Blunt, Sticky), DAM / DCM, number of cleavage sites of target sequence, selection of restriction enzyme.

• Frame Lane is a lane displaying areas where stop codons do not appear consecutively for each of six frames.
• For each of six frames, the region from the stop codon to the stop codon indicates the region with the specified number of codons or more.
• You can register as a new feature by right-clicking an area where stop codon does not exist.

Expression Profile Lane is a lane displaying gene expression profile. (Implemented in Array Edition)

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.

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.

• It is a function to search annotations by entering keywords.
• Multiple target feature keys can be selected.
• Multiple keywords can be specified and logical operations between keywords can be selected by AND / OR / NOT.
• Search scope can be limited to CDS area and Inter Genic area separately.
• On the search results screen, buttons for feature key number, position on sequence, base length, gene name, base sequence, button to annotation to descriptions are listed, CDS shows weekly amino acid sequence, + chain
• You can perform operations such as display selection only for chains, delete all at once, display codon table, search and add sequence number to features, transfer list to FusionPCR function.
• When you click on the row in the results list, the main feature map will display a map of that feature - position.
• You can output files in CSV / FastA / GenBank format. 
• Qualifier batch deletion is also implemented.

• Select multiple registered array patterns and detect patterns existing in the current array.
• It is also possible to search by entering new patterns when searching.
• The search range can be specified and the search target strand can also be specified.
• Mismatch detection of 1 to 2 letters is possible.
• You can also specify the search region of the CDS region or intergenic region.
• It is possible to search only upstream / downstream designated areas of CDS.
• In addition, multiple arrays can be set as search targets.
• On the search results screen, you can display the detected number, the position on the sequence, and the genes upstream and downstream for each pattern.
• In addition, results can be automatically registered as new features.
• The result can be output as file in CSV / FastA format.
• When you click on a row in the search result list, the main feature map moves so that the position of the pattern is at the center of the map, and the corresponding pattern array on the array lane is highlighted.

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.

There are the following methods to specify query sequenses.

• Enter the query sequence directly
• Paste query sequence
• Refer to the query sequence file saved as a file
• Right click on one feature on the main feature lane and make the sequence of that feature - the query array
• Right click on one feature on the reference feature map and make the sequence of that feature - the query array
• Sequence of all the features in the selection area of main feature lane (selectable by mouse drag) as query sequence (multiple queries): implemented GE AE DS GT

The database for search has the following.

• Genomic base sequence (including amino acid sequence on CDS) loaded in current reference feature map
• Registered genome base database or amino acid sequence database
• NCBI base sequence database or amino acid sequence database

You can select the search program from the following.

• BlastN
• BlastP
• BlastX
• tBlastN
• tBlastX

Homology search is performed in bacth and mass with all the features present in the designated genomic region as query sequences.

• A viewer that displays a sequence of the area currently displayed in the main feature map.
• You can display the display range on the viewer, show / hide the reverse strand, display / not display the amino acid translation, change the display method of the scale, display number of bases displayed.
• You can output image files in PDF, PNG, EMF format respectively.

• Editing / deleting of profile concentric circles, addition / editing / deletion of profile concentric circles, automatic map creation of multiple genomes, printing · image file output (PDF, PNG, EMF) is possible.
• The designed circular layout can be saved as a layout style and another genome sequence can be created with similar design.
• You can add concentric circles of various styles to the map.
• For one concentric circle, you can display and set multiple features, and you can specify strand designation, color classification, only specified features.
• Also, you can freely set the resolution such as content map such as GC content.
• It is also possible to draw by sequentially switching genomic sequences loaded in the current directory.
• You can change map resolution, diameter, phone size, and map name.

• It is similar to the circular genome map editor, but draws a relatively small circular genome.
• The annular lanes are arranged concentrically, and you can place multiple feature keys on one concentric circle.
• Strand, frame, feature shape, color designation of fill and frame, thickness of frame, selection of color classification, display / non-display of label, selection of Qualifier to be used as a label, font size, two concentric circle overlay functions ,
• You can change the scale interval.
• Designed styles can be saved and applied to other plasmids.
• You can change the order of concentric circles, add / delete, and edit.
• Plasmid maps can be output in three types of image formats: PDF, PNG, and EMF.

• It is a viewer / editor which is used when reading output file from ABI, SCF capillary sequencer.
• Not only the base sequence, but also its waveform (trace) can be displayed.
• You can change the base call.

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.

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

• Register primers from the sequence lane
• Register primers from the feature lane

Ability to design features on the feature lane and primers to amplify inside and outside the selected area

• Primer design for amplifying included products, including selected features of feature lanes
• Primer design for amplifying the product containing or containing the selected genomic region of the feature lane

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)

• Batch PCR Primer Design Batch PCR primer design to amplify all features with specified feature key on genome
• Whole Genome Covering PCR Primer Design PCR primer design that PCR product completely overlaps whole genome or large genomic region with PCR product overlapping
• Sequencing Primer Design PCR primer design for sequencing DNA fragments that can not be covered with one lead of a capillary sequencer
  reference

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.

• In-Fusion Design Ver.1: Primer design function for In-Fusion Cloning
• In-Fusion Design & Build Ver.2: Primer design function for In-Fusion Cloning
• In-Fusion Design & Build Ver. 3: Ability to design and build gene clusters by dropping DNA fragments to be inserted into vector sequences
• Batch Gene Cluster Design & Build: the ability to design and build lumped numerous gene clusters by replacing the gene sets that make up the cluster
• Combinatorial Design & Build: The ability to combinatorially combine design and build a fragment constituting a gene cluster

Purpose and overview

• Ligation is an essential experiment to perform molecular cloning. IMC combines various nucleotide sequences including annotated nucleotide sequences with each other in the same manner as in actual cloning experiments to generate the products. All annotations are properly succeeded also to the ligation products and their products can be analyzed using many functions of the IMC as well as the original base sequence.

Function

• If the terminal sequences complementarily match each other, ligate them into one base sequence.
• Up to 5 fragment segments can be ligated.
• You can generate all possible ligation sequences.
  • In Version 7.24 and later, the complete complementary sequence of the ligation product is counted as a separate product.
• Annotated nucleotide sequences of GenBank and EMBL format can be ligated as well, and these annotations are properly inherited by the ligation products.
• If the shapes and sequences of the ends of the base sequence complementarily match, a circular base sequence is generated.
• It displays a list of restriction enzymes that can be used to check the insert direction of each fragment in the generated ligation product.
  • Also displays gel electrophoresis pattern when using these restriction enzymes.
• Displays the terminal shape of all base sequences loaded in the current folder.

• The base sequence generated as a ligation product can be analyzed in the same way as the original base sequence.

Restrictions

• Currently, ligation linking 6 or more base sequences is not possible.

Algorithm

• For restriction enzyme cleaved sequences on IMC, special Feature Keys and Qualifiers are generated that indicate the terminal status.

This function is installed in the following software

IMCGE

IMCAE

GenomeTraveler

• Multiple Linear Genome Map (Multiple Linear Genome Map) is a function to comparatively draw Feature from multiple genomic chromosomes between closely related species in parallel.
• Homology search can be performed on all the features on other genomes by right clicking one feature on the multiple linear genomic map and if that feature has homologous clan strings on other genomes, homologous genes Alignment can be displayed on the axis.
• "IMC O10 Gene Cluster Alignment" can be executed by right mouse click from multiple linear map.
• You can output files in PDF, PNG, and EMF image formats.

• This function is implemented in the following editions.
  • IMCGE, AE, DS, GT
• We display homology regions between two genomic sequences in dot matrix.

• Select and compare the current genome sequence and one genomic sequence loaded in the current reference directory.
• You can set dot color by Overlap base length,% Identity level.
• In the result display window, zooming, shifting, enlarging an arbitrary region selected by rectangle, dot color setting, navigation window, restriction on the number of display dots, and feature key display (display of annotations with feature - mouse-over) are possible.
• A dot image can be output as a file in PDF / PNG / EMF format, and print setting is also possible.
• The dot list can be output as a file in CSV format.

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 level

It is a function to check if the gene cluster is designed correctly.

• Does it possess a gene composition, codon composition that matches the composition of the host
• Is the start codon and the stop codon correct?
• Is there a required array?
  
  • Restriction enzyme recognition site
  • RBS
  • Homology Arm
• Is there an unnecessary array
  
  • Restriction enzyme recognition site