Sequerome is a web-based

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’ an ...

for integrating the results of a

BLAST Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

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 Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...

tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

and

nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...

analysis. Since its inception in 2005, the tool has been featured in ''

Science Science is a systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the universe. Science may be as old as the human species, and some of the earliest archeological evidence for ...

''"A Bigger BLAST", NetWatch
Science
VOL 309, 23 Sep 2005, p-1971 ,"Seq and Find" and officially linked to many

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

portals around the globe.

Description

Sequerome has the following features: profiling Sequence alignment reports from

by linking the results page to a panel of third party services,

tabbed browsing In interface design, a tab is a graphical user interface object that allows multiple documents or panels to be contained within a single window, using tabs as a navigational widget for switching between sets of documents. It is an interface ...

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. Sanjeev Dappa, a

Tamil Tamil may refer to: * Tamils, an ethnic group native to India and some other parts of Asia **Sri Lankan Tamils, Tamil people native to Sri Lanka also called ilankai tamils **Tamil Malaysians, Tamil people native to Malaysia * Tamil language, nativ ...

researcher criticised Sequerome and when questioned, provided no further details.

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 BLAST 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.

Results Pane

Sequerome directly queries the input sequence against a variety of databases/tools ('popular public domains' and 'privately hosted services') including BLAST,

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

(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 PDBid), 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, PDBids 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,

PyMOL PyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become ...

, Rasmol, etc.) 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 ORF or Orf may refer to: * Norfolk International Airport, IATA airport code ORF * Observer Research Foundation, an Indian research institute * One Race Films, a film production company founded by Vin Diesel * Open reading frame, a portion of the ...

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

. 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 servlet A Jakarta Servlet (formerly Java Servlet) is a Java software component that extends the capabilities of a server. Although servlets can respond to many types of requests, they most commonly implement web containers for hosting web application ...

and Server Page technologies with

Java database connectivity Java Database Connectivity (JDBC) is an application programming interface (API) for the programming language Java, which defines how a client may access a database. It is a Java-based data access technology used for Java database connectivity. I ...

(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 (formerly Microsoft Internet Explorer and Windows Internet Explorer, commonly abbreviated IE or MSIE) is a series of graphical user interface, graphical web browsers developed by Microsoft which was used in the Microsoft Wind ...

and can be run on most operating systems equipped with a

Java Virtual Machine A Java virtual machine (JVM) is a virtual machine that enables a computer to run Java programs as well as programs written in other languages that are also compiled to Java bytecode. The JVM is detailed by a specification that formally describes ...

(JVM) and

Jakarta Tomcat Apache Tomcat (called "Tomcat" for short) is a free and open-source implementation of the Jakarta Servlet, Jakarta Expression Language, and WebSocket technologies. It provides a "pure Java" HTTP web server environment in which Java code can als ...

server. End-users have to download plugins for viewing structure of molecules from the Protein Data Bank (e.g. PyMOL, Cn3D, Rasmol, SwissPDB, etc.).

Further directions

The "post-

genomics Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

" era has given rise to a range of web-based tools and software to compile, organize, and deliver large amounts of

primary sequence Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length sc ...

information, as well as protein structures, gene annotations,

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. Alig ...

s, and other common bioinformatics tasks. A simple web-search returns any number of such services and software tools.