botany software

SUBMITTED TO: Mr. INAM-UL-HAQ Submitted By: Humna Ahmad Roll# 1067 B.S –botany – morning 3rd semester

UNIVERSITY OF EDUCATION Renala campus

GENOLOGICS & JaMBW

Data EntryDescription:The ways by which information is entered in a electronically manageable form depends on the tools used for producing the information. Sequences are either determined using radioactive methods, thus the result is an autoradiogram which is generally read manually or by a digitizer, or are determined by non-radioactive methods which involve robots like the Sequenator.

TOOLS

Tools are described in order to allow such a data entry process and conversion to different formats.

Sequence format conversion: SeqIO (James Knight)

Data ManipulationDescription:This section of the JaMBW package describes tools available for the commonest operations performed on sequence data.

Reverse / Complement / Inverse your sequence (Luca Toldo) 2.2Shuffle [randomize its order] your sequence (Luca Toldo) 2.3Translate from DNA to protein (Luca Toldo)

Reverse,Complement, Inverse

Aim: Given a sequence of nucleic acids, this program generates its reverse, its complement, and its inverse into three independent windows. The above mentioned terminology is explained with the following example: 5' ATATATCCCGGCG 3' input sequence

Mode Of Operation

This program uses 4 windows: the top one should be filled from the user, with a sequence of interest, while the other 3 windows contain the results of the operations. The following steps must be performed: Sequence input .Symbols used Either paste or type in the top area the sequence of interest. Any character or symbol that does not belong to the IUB [atcgATCG] set is ignored.

. removal of header information

Only the sequence must be placed in the top window: heading comments must be removed.. long sequences and small window

In order to allow users with small screens to still be able of using this program, the size of each window had been made rather small. Therefore, use the scroll-bars in order to move around in the input and output windows. The suggested strategy is to double click in the specified area and then do copy/paste from/to the text-editor of choice or across different applications.

Case sensitivity choice:

Often is useful to mark regions of interest by changing the Case. This applet is capable of keeping those modifications also in its output, as well as to change the case of the sequence according to your wish. Therefore, by selecting anyone of the 3 choices provided, and hereafter described, the user has control on this aspect. In order to choose the case in the output, the following selections are possible, by clicking on the button close to them:

.Unchanged: leaves the same case in the output as in the input, and is useful for easier identification of already marked regions in the sequence .Upper: generates as output the upper case conversion (e.g. atcg becomes ATCG) .Lower: generates as output the lower case conversion (e.g. ATCG becomes atcg) Convert:Once the sequence is placed in the top window, by pressing the "CONVERT" button then the conversion is performed.  

How to understand its output :

Since both aim and mode of operation are rather straightforward, also the understanding and the use of the results from this work should not present any major difficulty. The output will simply consist of the same sequence reverse, complemented and inverted as in the examples shown above.

Randomize your Sequence

Aim: Given a sequence (of nucleic acids or aminoacids), this program generates a new version of it consisting of the same symbols but in a randomized order. This is explained with the following example TODAYISANICEDAY input sequenceSDEAAIDYOTIYACN output randomized order 

 Use of a randomized sequence is especially important when evaluating results of alignments (usually results of database searches) giving weak homologies. In such cases is "good practice" to perform subsequently a second search, but using a randomized version of the sequence and then compare the results obtained in the two runs.

Mode Of Operation

This program uses 2 windows: the top one should be filled from the user, with a sequence of interest, while the other window contains the result of the randomization. The following steps must be performed:

Sequence input

Symbols used:Either paste or type in the top area the sequence of interest. Any character or symbol that does not belong to the [a-zA-Z] set is ignored.

. removal of header information:

Only the sequence must be placed in the top window: heading comments must be removed long sequences and small window:

In order to allow users with small screens to still be able of using this program, the size of each window had been made rather small. Therefore, use the scroll-bars in order to move around in the input and output windows. The suggested strategy is to double click in the specified area and then do copy/paste from/to the text-editor of choice or across different applications.

Case sensitivity choice:

Often is useful to mark regions of interest by changing the Case. This applet is capable of keeping those modifications also in its output, as well as to change the case of the sequence according to your wish. Therefore, by selecting any one of the 3 choices provided, and hereafter described, the user has control on this aspect. In order to choose the case in the output, the following selections are possible, by clicking on the button close to them:

Unchanged: leaves the same case in the output as in the input, and is useful if one wants to easier identify already marked regions of the sequence Upper: generate as output the upper case conversion (e.g. atcg becomes ATCG) Lower: generate as output the lower case conversion (e.g. ATCG becomes atcg)Shuffle:Once the sequence is placed in the top window, by pressing the "SHUFFLE" button then the conversion is performed.

How to understand its output :

Since both aim and mode of operation are rather straightforward, also the understanding and the use of the results from this work should not present any major difficulty. In fact, the output will consist of simply a sequence with the same composition as the input but in a fully unpredictable order.

Data AnalysisThis section of the JaMBW package describe tools available for the commonest operations performed on data analysis. Single Sequences Windowed percentage composition(Luca Toldo) Feature Viewer (Luca Toldo) Look at all possible ORF (Luca Toldo) Isoelectric point (Luca Toldo) Antigenicity index (Luca Toldo and Ramu Chenna) Oligo Calculator (Eugen Buehler) Pairs of Sequences dotplot comparisons(Luca Toldo)

Oligo Calculator

Reference

Doelz, R.(1990) BioCompanion, Biocomputing Essentials series, ISBN 3-905 434-00-8 Author:Luca I.G. TOLDO, Edition date: 28 February 1997   

  Watson,J.D. and Crick,F.H.C.(1953) Genetical implications of the structure of deoxyribonucleic acid. Nature,171,964-967. Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1985) Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984.Eur-J-Biochem,150,1-5 Author:Luca I.G. TOLDO, Edition date: 28 February 1997