2008
DOI: 10.1186/1471-2105-9-121
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Abstract: BackgroundThe exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive for completeness, the range of user interests is often beyond their scope. Large databases covering a broad range of domains tend to offer less detailed information than smaller, more specialized resources, often creating a need to combine data from many sources in order to obtain a complete pictu… Show more

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Cited by 18 publications
(10 citation statements)
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References 17 publications
(11 reference statements)
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“…The MilkAMP database was implemented on the Linux platform with MySQL (v5.1.62) and Apache (v2.2.2.1), while the Web interface was implemented with PHP (v5.2.17). Sequences were retrieved in SciDBMaker (Hammami et al 2008), compiled and the resulting tables exported to the MySQL server. MilkAMP includes numerous tools for sequence analysis, such as homology search (BLAST v2.2.15 (Altschul et al 1997), FASTA v35.04 (Pearson and Lipman 1988) and Smith-Waterman v35.04 (Pearson and Lipman 1988)), multiple sequence alignment (ClustalW v2.10 (Larkin et al 2007), MUSCLE v3.6 (Edgar 2004)), Hidden Markov Models (HMMER v2.3.2 (Durbin et al 1998)), and physicochemical profile analyzer.…”
Section: Methodsmentioning
confidence: 99%
“…The MilkAMP database was implemented on the Linux platform with MySQL (v5.1.62) and Apache (v2.2.2.1), while the Web interface was implemented with PHP (v5.2.17). Sequences were retrieved in SciDBMaker (Hammami et al 2008), compiled and the resulting tables exported to the MySQL server. MilkAMP includes numerous tools for sequence analysis, such as homology search (BLAST v2.2.15 (Altschul et al 1997), FASTA v35.04 (Pearson and Lipman 1988) and Smith-Waterman v35.04 (Pearson and Lipman 1988)), multiple sequence alignment (ClustalW v2.10 (Larkin et al 2007), MUSCLE v3.6 (Edgar 2004)), Hidden Markov Models (HMMER v2.3.2 (Durbin et al 1998)), and physicochemical profile analyzer.…”
Section: Methodsmentioning
confidence: 99%
“…Physicochemical data of anti-MRSA peptides were determined by Scientific DataBase Maker software (Hammami et al 2008) including length (L), mass (M), isoelectric point (pI), net charge (NC), hydrophobicity (HP), basic (Br), acidic (Ar), hydrophobic (Hr) and polar residues (Pr), boman index (Bi), instability index (Ii), aliphatic index (Ai), carbon (Cn), azot (An), hydrogen (Hn) and oxygen number (On). The minimum, mean and maximum values of selected physicochemical properties of the analysed anti-MRSA peptides are presented in Table 2.…”
Section: Physico-chemical Characteristicsmentioning
confidence: 99%
“…To identify strand specific divergence in different sequenced strains, the isoelectric point (pI) distribution were calculated using the SciDB maker [35].…”
Section: Determination Of Isoelectric Point (Pi) Distribution Of the mentioning
confidence: 99%