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FAIR: A server for internal sequence repeats.

Senthilkumar R, Sabarinathan R, Hameed BS, Banerjee N, Chidambarathanu N, Karthik R, Sekar K - Bioinformation (2010)

Bottom Line: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences.Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases.The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, Indian Institute of Science, Bangalore 560 012, India.

ABSTRACT

Unlabelled: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases. The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases. The server is freely accessible over the World Wide Web (WWW).

Availability: http://bioserver1.physics.iisc.ernet.in/fair/

No MeSH data available.


Related in: MedlinePlus

FAIR server output of identical repeats in the protein sequence from Mycobacterium tuberculosis H37Rv.
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Related In: Results  -  Collection


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Figure 1: FAIR server output of identical repeats in the protein sequence from Mycobacterium tuberculosis H37Rv.

Mentions: Figure 1 displays a sample output for an input (FASTA format)protein (probable polypeptide synthase pks12) sequence fromMycobacterium tuberculosis H37Rv. Identification of repeats inpolyketide synthase would be of immense importance as it is animportant target for drug designing. The total number of amino acidresidues in the input sequence is 4151 (only part of the input is shownin Figure 1). The minimum number of residues in the repeat is set tobe greater than or equal to 120. The results produced by the computingserver are shown in Figure 1. The computing engine found three longidentical repeats of 215, 128 and 307 length (Figure 1). The results ofthe proposed server are compared with the SWELFE server for theabove input sequence and are reported in Table 1 (see supplementary material). It is interesting to note that the proposed server identifiedmany identical internal repeats whereas the SWELFE reported onlysimilar repeats (see Table 1 in supplementary materialfor details).


FAIR: A server for internal sequence repeats.

Senthilkumar R, Sabarinathan R, Hameed BS, Banerjee N, Chidambarathanu N, Karthik R, Sekar K - Bioinformation (2010)

FAIR server output of identical repeats in the protein sequence from Mycobacterium tuberculosis H37Rv.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2957760&req=5

Figure 1: FAIR server output of identical repeats in the protein sequence from Mycobacterium tuberculosis H37Rv.
Mentions: Figure 1 displays a sample output for an input (FASTA format)protein (probable polypeptide synthase pks12) sequence fromMycobacterium tuberculosis H37Rv. Identification of repeats inpolyketide synthase would be of immense importance as it is animportant target for drug designing. The total number of amino acidresidues in the input sequence is 4151 (only part of the input is shownin Figure 1). The minimum number of residues in the repeat is set tobe greater than or equal to 120. The results produced by the computingserver are shown in Figure 1. The computing engine found three longidentical repeats of 215, 128 and 307 length (Figure 1). The results ofthe proposed server are compared with the SWELFE server for theabove input sequence and are reported in Table 1 (see supplementary material). It is interesting to note that the proposed server identifiedmany identical internal repeats whereas the SWELFE reported onlysimilar repeats (see Table 1 in supplementary materialfor details).

Bottom Line: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences.Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases.The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, Indian Institute of Science, Bangalore 560 012, India.

ABSTRACT

Unlabelled: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases. The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases. The server is freely accessible over the World Wide Web (WWW).

Availability: http://bioserver1.physics.iisc.ernet.in/fair/

No MeSH data available.


Related in: MedlinePlus