Sequerome
Encyclopedia
Sequerome is a web-based Sequence profiling tool
for integrating the results of a BLAST
sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. Sequerome is a web based Java tool that acts as a front-end to BLAST
queries and provides simplified access to web-distributed resources for protein
and nucleic acid
analysis.
Since its inception in 2005, the tool has been featured in Science
and officially linked to many bioinformatics
portals around the globe.
Sequerome has the following features: profiling Sequence alignment reports from BLAST
by linking the results page to a panel of third party services, tabbed browsing allowing user to come back earlier operations, visit third party services to perform customized sequence manipulations, one-box any-format sequence input and alternate options for sequence input including visiting third party sites, cached storage of input sequences and retrieval, a three pane browsing environment allowing simultaneous input and analysis of multiple sequences, and archival options on top of each icon, for results from each pane
The software application can be accessed directly. The homepage shows three panels: Query pane, Results pane and the Search History pane. The user may resize these panes to perform parallel actions in any of these panes. In a single browser it is possible to run parallel BLAST
searches on different sequences, analyzing them or viewing the restriction digests for each document of a BLAST
result
the sequence right away under standard parameters. Experienced users have a choice to perform further special operations under the Advanced options. Some of features include selection of specific databases to BLAST
from, upload facility to work with FASTA files stored in individual computers, sequence retrieval using NCBI IDs and visit any user-defined URL to drag-N-drop the sequences. Alternatively the user can also perform a variety of other actions including Sequence manipulation, analysis, and alignment using existing tools available in the web. The One-box any-sequence, takes input in any format (FASTA, with or without spaces/numbers...). Alerts also exist to warn wrong selection of choices (DNA/RNA/Protein). Results obtained from 'sequence manipulation' e.g. translation, can be further carried on to do further BLAST
analysis while preserving the history of the earlier search.
, PDB
, REBASE and others, and generates outputs that are intuitive and easily comprehensible. Access to various analysis tools, (including viewing a 3D structure-viewer from a PDB
id), is provided as separate command buttons to analyze every record from a BLAST
report before making a final selection. In case of results from a protein BLAST
, PDB
ids are displayed prominently in appropriate cases next to the BLAST
record, so that the structure of the molecule with a match can be viewed directly (with an already downloaded version of molecular structure viewer e.g. Cn3D
, ‘Rasmol’.... Once the BLAST
report is displayed on the Results pane, the user can to directly perform an analysis on any of the BLAST
hits using a series of command buttons that are linked to the respective servers/ sites. Most of the results from third party servers can be viewed directly in the Results pane without opening up as many browsers e.g. ORF
prediction, Protparam.
and Server Page technologies with Java database connectivity
(JDBC), making it both server and platform-independent. Sequerome is compatible with essentially all Java-enabled, graphical browsers but is better accessed using Internet Explorer
and can be run on most operating systems equipped with a Java Virtual Machine
(JVM) and Jakarta Tomcat server. End-users have to download plugins for viewing structure of molecules from PDB
e.g. Cn3D, Rasmol, SwissPDB etc.
" era has given rise to a range of web based tools and software to compile, organize, and deliver large amounts of primary sequence information, as well as protein structures
, gene annotations, sequence alignment
s, and other common bioinformatics tasks. A simple web-search returns any number of such services and software tools.
Sequence profiling tool
A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to...
for integrating the results of a BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. Sequerome is a web based Java tool that acts as a front-end to BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
queries and provides simplified access to web-distributed resources for protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
and nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
analysis.
Since its inception in 2005, the tool has been featured in Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
and officially linked to many bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
portals around the globe.
Description
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
by linking the results page to a panel of third party services, tabbed browsing allowing user to come back earlier operations, visit third party services to perform customized sequence manipulations, one-box any-format sequence input and alternate options for sequence input including visiting third party sites, cached storage of input sequences and retrieval, a three pane browsing environment allowing simultaneous input and analysis of multiple sequences, and archival options on top of each icon, for results from each pane
The software application can be accessed directly. The homepage shows three panels: Query pane, Results pane and the Search History pane. The user may resize these panes to perform parallel actions in any of these panes. In a single browser it is possible to run parallel BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
searches on different sequences, analyzing them or viewing the restriction digests for each document of a BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
result
Query Pane
Each browser session can be initiated perform without asking too many questions at the outset. The user has to just dump in the sequence in the Query pane, and BLASTBLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
the sequence right away under standard parameters. Experienced users have a choice to perform further special operations under the Advanced options. Some of features include selection of specific databases to BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
from, upload facility to work with FASTA files stored in individual computers, sequence retrieval using NCBI IDs and visit any user-defined URL to drag-N-drop the sequences. Alternatively the user can also perform a variety of other actions including Sequence manipulation, analysis, and alignment using existing tools available in the web. The One-box any-sequence, takes input in any format (FASTA, with or without spaces/numbers...). Alerts also exist to warn wrong selection of choices (DNA/RNA/Protein). Results obtained from 'sequence manipulation' e.g. translation, can be further carried on to do further BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
analysis while preserving the history of the earlier search.
Results Pane
Sequerome directly queries the input sequence against a variety of databases/tools (‘popular public domains’ and ‘privately hosted services’) including BLASTBLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
, PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, REBASE and others, and generates outputs that are intuitive and easily comprehensible. Access to various analysis tools, (including viewing a 3D structure-viewer from a PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
id), is provided as separate command buttons to analyze every record from a BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
report before making a final selection. In case of results from a protein BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
, PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
ids are displayed prominently in appropriate cases next to the BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
record, so that the structure of the molecule with a match can be viewed directly (with an already downloaded version of molecular structure viewer e.g. Cn3D
Cn3D
Cn3D is a Windows, Macintosh and Unix-based software from the United States National Library of Medicine that acts as a helper application for web browsers to view three-dimensional structures from The National Center for Biotechnology Information's Entrez retrieval service...
, ‘Rasmol’.... Once the BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
report is displayed on the Results pane, the user can to directly perform an analysis on any of the BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
hits using a series of command buttons that are linked to the respective servers/ sites. Most of the results from third party servers can be viewed directly in the Results pane without opening up as many browsers e.g. ORF
Open reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
prediction, Protparam.
Search History Pane
One of the key features of a profiling an input sequence data is to store, retrieve and effectively combine and re-use the older inputs. These can be further enhanced if there is retrieval options for each of the operations performed. The bottom right panel in the browser does this while also storing all the input sequences entered earlier. Thus the browser lends an environment to carry out tabbed browsing.. For each of the icons linking to the stored results, the user has a choice of archiving them, including print, save and mail options. These can be seen as small colored pictures on top of each icon.Implementation
Sequerome has a three-tiered architecture that uses Java servletJava Servlet
A servlet is a Java programming language class used to extend the capabilities of servers that host applications accessed via a request-response programming model. Although servlets can respond to any type of request, they are commonly used to extend the applications hosted by Web servers...
and Server Page technologies with Java database connectivity
Java Database Connectivity
Java DataBase Connectivity, commonly referred to as JDBC, is an API for the Java programming language that defines how a client may access a database. It provides methods for querying and updating data in a database. JDBC is oriented towards relational databases...
(JDBC), making it both server and platform-independent. Sequerome is compatible with essentially all Java-enabled, graphical browsers but is better accessed using Internet Explorer
Internet Explorer
Windows Internet Explorer is a series of graphical web browsers developed by Microsoft and included as part of the Microsoft Windows line of operating systems, starting in 1995. It was first released as part of the add-on package Plus! for Windows 95 that year...
and can be run on most operating systems equipped with a Java Virtual Machine
Java Virtual Machine
A Java virtual machine is a virtual machine capable of executing Java bytecode. It is the code execution component of the Java software platform. Sun Microsystems stated that there are over 4.5 billion JVM-enabled devices.-Overview:...
(JVM) and Jakarta Tomcat server. End-users have to download plugins for viewing structure of molecules from PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
e.g. Cn3D, Rasmol, SwissPDB etc.
Further directions
The "post-genomicsGenomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
" era has given rise to a range of web based tools and software to compile, organize, and deliver large amounts of primary sequence information, as well as protein structures
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
, gene annotations, sequence alignment
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
s, and other common bioinformatics tasks. A simple web-search returns any number of such services and software tools.