Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Using FlyBase to Find Functionally Related Drosophila Genes

doi: 10.1007/978-1-4939-7737-6_16

Figure Lengend Snippet: (a) The Gene Ontology (GO) tab of the QuickSearch tool. (b) The Vocabularies tool page, which offers two search options: a search term box (top) and a browsing window to select top-level GO terms (bottom).

Article Snippet: A list of D. melanogaster genes whose product(s) contain a specified protein domain (as defined by InterPro signatures) can be obtained by using the “Protein Domains” tab of the QuickSearch tool.

Techniques:

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Using FlyBase to Find Functionally Related Drosophila Genes

doi: 10.1007/978-1-4939-7737-6_16

Figure Lengend Snippet: (a) The Protein Domains tab of the QuickSearch tool. (b) The “Families and Domains and Molecular Function” section of a Gene report, which includes information on protein domains and Gene Group membership. The gene CASK is shown as an example.

Article Snippet: A list of D. melanogaster genes whose product(s) contain a specified protein domain (as defined by InterPro signatures) can be obtained by using the “Protein Domains” tab of the QuickSearch tool.

Techniques:

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Using FlyBase to Find Functionally Related Drosophila Genes

doi: 10.1007/978-1-4939-7737-6_16

Figure Lengend Snippet: (a) The Gene Groups tab of the QuickSearch tool. (b) Gene Groups are available as a browsable list. Groups are displayed as a nested hierarchy, with the top-level groups arranged in alphabetical order. The top section of the list is shown from ACETYLCHOLINE RECEPTORS to AUTOPHAGY-RELATED GENES. (c) A Gene Group report, using the ACTINS Gene Group as an example.

Article Snippet: A list of D. melanogaster genes whose product(s) contain a specified protein domain (as defined by InterPro signatures) can be obtained by using the “Protein Domains” tab of the QuickSearch tool.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

doi: 10.3390/ijms23020642

Figure Lengend Snippet: The detailed genes information of ClPRXs.

Article Snippet: Online information at http://h-s.p-443.npsa-prabi.ibcp.fr.neau.vpn358.com/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_gor4.html (accessed on 2 April 2021) for protein secondary structure prediction was retrieved using softberry web online tools ( http://linux1.softberry.com/berryPHTML?Topic=protcomppl&group=programs&group=Proloc (accessed on 2 April 2021)) and finally used to predict the subcellular localization of 79 ClPRX proteins.

Techniques: Molecular Weight

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

doi: 10.3390/ijms23020642

Figure Lengend Snippet: Structural characteristics of ClPRX protein. ( A ) Schematic diagram of the primary structure of the class III peroxidase. The green boxes at the front and back signify the N-terminal signal peptide (SP) and c-terminal extension domain (CT). The middle three boxes represent the highly conserved domain: box I is the distal-heme-binding site domain; box Ⅱ is the unknown functional domain; box Ⅲ is the proximal-heme-binding site domain. The gray area with obvious variation was assumed to be a variable domain responsible for the specific catalytic function of peroxidase. The highly conserved distal histidine (Hd) and proximal histidine (HP) are heme-binding sites represented by green bars. Eight cysteines (C1–C8) are key amino acids that form disulfide bonds to form the secondary structure of peroxidase, which are represented by yellow solid circles. The four conserved disulfide bonds formed are shown as black lines in plane. ( B ) represents the four conserved domains and site location information of the third type of peroxidase, which are marked on the amino acid sequence with four different colors, and the 3D model of the structure of the four domains is displayed, the yellow part being the functional site. ( C ) is the comparison results of 7 groups of ClPRX protein sequences.

Article Snippet: Online information at http://h-s.p-443.npsa-prabi.ibcp.fr.neau.vpn358.com/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_gor4.html (accessed on 2 April 2021) for protein secondary structure prediction was retrieved using softberry web online tools ( http://linux1.softberry.com/berryPHTML?Topic=protcomppl&group=programs&group=Proloc (accessed on 2 April 2021)) and finally used to predict the subcellular localization of 79 ClPRX proteins.

Techniques: Binding Assay, Functional Assay, Sequencing, Comparison