FAQs

Genchek™

Q. What is a Sublist ?
A. A sublist is a logical grouping of sequences. A sublist may group together sequences that have been imported from a particular location or sequences that have a biological relation or sequences that are a part of a particular project. The grouping of sequence is left to the discretion of the user.

Q. Why are some menu options disabled though a sequence is selected in the Data Browser?
A. The menu options in Genchek™ are enabled depending on the type and number of sequences selected in the data browser.

Q. Is there any restriction on the numbers of sequences to be imported ?
A. No, Genchek™ has no restriction on the number of sequences that can be imported simultaneously. It will depend on the computer specifications on which Genchek™ is running.

Q. What data formats does Genchek™support?
A. Fasta, GenBank. EMBL, Text, SCF, ABI, DDBJ.

Q. What are the different ways of importing sequences in Genchek™ ?
A. You can load sequences into Genchek™ from the Add Sequence menu option of the Sequence menu or by direct click on the import icon. Click 'From System' to load sequences from a text file in your local drive. To import sequences of known accession numbers or gi numbers from NCBI click 'From Entrez'.

Q. I don't see my file when I click on browse button to import file from system ?
A. Check the file format you want to import and set File Of Type field accordingly. If the format is not supported by Genchek™ then an Error message pops up.

Q. I have a sequence data from an automated sequencer. How do I use the data in the Genchek™Application ?
A. Genchek™ allows import of an electropherogram ( chromatogram ) from a sequencing machine. A user can trace all standard electropherograms ( e.g. *.abi, *.scf ) . Genchek™ also allows a researcher to rescale an image, edit a sequence, clip noisy peaks and convert an electropherogram data to text format.

Q. If sequences include U (Uracil), can they still be processed?
A. Yes, even a sequences that includes U can be processed.

Q. Does Genchek™ support export of files in image format ?
A. Yes, Genchek™ supports the export of output files as images as well as in text format.

Q. How can I add Restriction Enzymes to the list?
A. To add an enzyme to a sublist, right click on the existing list and select Create . A new window opens. Enter the recognition sequence and cutting position and click Save button to add the enzyme to the existing list.

Q. Is there a Network version ? How does it work? Or, How can I run Genchek™ on several machines without having to move the copy protection key all the time?
A. We have network compatible programs for all the operating systems. Only one copy protection key is needed and that can be placed on any computer on your network. The key server program monitors the number of users running the Genchek™ program across the network.

Q. What are Proxy Settings?
A. In an enterprise that uses the Internet, a proxy server is a server that acts as an intermediary between a workstation/user and the Internet so that the enterprise can ensure security, administrative control, and caching service. A proxy server is associated with or part of a gateway server that separates the enterprise network from the outside network as well as a firewall server that protects the enterprise network from outside intrusion. Proxy settings in Genchek™ involves IP address of the proxy server of the organization and its port number.

Q. When do I need to set proxy?
A. You need to set proxy in case you/ your organization is connected to the Internet through a proxy server.

Q. What is a port? Should the port always be 2001?
A. Ports provide a means by which computers communicate with one another using standard protocols. Each protocol is assigned to a fixed port number so that the computers know which port to check in order to communicate using the specified protocol. When you start up a program that will communicate with remote computers using a specific protocol, the port assigned to that protocol is the one that it will use to attempt to communicate. The port number being used needs to be the same on each computer attempting to communicate in order that the message packets sent by the one computer are correctly received and recognized by the other. Port numbers fall into three ranges. Ports 0 through 1023 are called "Well Known Ports" and are assigned to their specified purpose by the Internet Assigned Numbers Authority (IANA). Ports 124 through 49151 are available for general use and may be registered with IANA if desired. Ports 49152 through 65535 are used where a dynamic or private port is required. You can protect your computer against some forms of attack over the Internet by restricting the ports that your computer allows other computers to use to communicate with it. For maximum security, you should ensure that access to all ports, except those that you need to use, are blocked.

Q. Why do I need to set the Local BLAST settings?
A. Basically, to be able to query your sequence against your local blast database.

Q. Where is my local database created?
A. Your local database is a collection of flat files containing sequences saved on your local drive where Genchek™ has been installed .

Q. Why should I create a local database?
A. You need to create a local database only if you want to search your query sequence against sequences that are proprietary or patented.

Q. Why is my BLAST server forever sending the sequence?
A. Check your Proxy settings in the Preferences option of System in the main menu. The proxy settings may need to be reset.

Q. Where should Local BLAST Manager be installed?
A. Local BLAST Manager should be installed in the same location where Genchek is installed. Install Local BLAST Manager in BLAST folder under Genchek installation folder. By default, this should be installed at C:\Genchek\BLAST (For Windows OS), /usr/local/bin/Genchek/BLAST(For Linux & Solaris OS), and /Genchek/BLAST(For Mac).

Q. Local BLAST gives zero hits. What should I do?
A. To avoid this, install Local BLAST Manager in the same location where Genchek is installed. Install Local BLAST Manager in BLAST folder under Genchek installation folder. By default, this should be installed at C:\Genchek\BLAST (For Windows OS), /usr/local/bin/Genchek/BLAST(For Linux & Solaris OS ), and /Genchek/BLAST(For Mac).

Q. “Illegal characters were removed. Database built with errors” message is displayed when I perform Local BLAST. Why do I get this message?
A. Database build might have invalid characters.

Q. When I try to create a Local BLAST database from Local BLAST Manager, I get this message “Error while creating Local BLAST Database” Why do I get this message?
A. Local BLAST Manager should be installed in the same location where Genchek is installed. Install Local BLAST Manager in BLAST folder under Genchek installation folder. By default, this should be installed at C:\Genchek\BLAST (For Windows OS), /usr/local/bin/Genchek/BLAST(For Linux & Solaris OS), and /Genchek/BLAST(For Mac).

Q. I tried creating Local BLAST Database using sequences from Genchek Data Browser. I get this message “Unable to format given database.” Why do I get this message?
A. Local BLAST Manager should be installed in the same location where Genchek is installed. Install Local BLAST Manager in BLAST folder under Genchek installation folder. By default, this should be installed at C:\Genchek\BLAST (For Windows OS), /usr/local/bin/Genchek/BLAST(For Linux & Solaris OS), and /Genchek/BLAST(For Mac).

Q. On selecting Local BLAST option in Select BLAST type dialog, a message 'Start Local BLAST Server from Local BLAST Manager' is seen. How should I start Local BLAST server?
A. Before using Local BLAST module, start Local BLAST Manager. If default selections are made while installing Local BLAST Manager, select Start > Programs > Local BLAST Manager - Ocimum Biosolutions > Local BLAST Manager (For Windows OS), /usr/bin/Local BLAST Manager - Ocimum Biosolutions/ Local BLAST Manager (For Linux/Solaris OS), and Applications > Local BLAST Manager - Ocimum Biosolutions > Local BLAST Manager (For Mac OS).

In Local BLAST Manager window, Click start button in Local BLAST Manager to start Local BLAST Server. Status Bar shows message “Server Started”.

Now you can go ahead and perform BLAST search on your local database.

Q. How should I start Local BLAST Manager?
A. If default selections are made while installing Local BLAST Manager, select Start > Programs > Local BLAST Manager - Ocimum Biosolutions > Local BLAST Manager (For Windows OS),  /usr/bin/Local BLAST Manager - Ocimum Biosolutions/ Local BLAST Manager (For Linux/Solaris OS), and Applications > Local BLAST Manager - Ocimum Biosolutions > Local BLAST Manager (For Mac OS).

Q. 'Internet connection failed. Check your internet connection.' message is displayed when I perform NCBI BLAST. Why do I get this message?
A. This could be due to two reasons. Firstly due to improper internet connection or due to spaces present in the name of the installation folder. To avoid getting this message, ensure proper internet connection and no spaces should be present in the name of the installation folder. By default, Genchek should be installed in C:\Genchek(For Windows OS), /usr/local/bin/Genchek(For Linux & Solaris OS), and /Genchek (For Mac).

Q. How can I evaluate Genchek™?
A. You can request the Free Evaluation Version by filling the Product Enquiry Form available on our site.

Q. Is there any feature which is restricted in the trial version?
A. User cannot change Login, create users and change password.

Q. Is there a live help support for Genchek™?
A. Genchek™ has a dedicated technical support staff to answer your queries. For live help just go to our site and click on Live Help, where you can chat LIVE with our experts regarding your queries.