Specific primers were designed based on the corresponding nucleotide sequence of identified proteins from CTDB (Chickpea Transcriptomic Database), DFCI (Medicago trancatula database), PDB (Protein data Bank) and NCBI database using Gene Runner software (version 3.1) and listed in Additional file 2. qRT-PCR was performed on Biorad i cycler (Bio-Rad I-Q5, USA) using SyBr green super mix.
Variation factors are as follows: (i) preposition introducing the location at/from/in/into/through/to/on/via/with/within; (ii) URL used (e.g. ~5 variants for GEO); (iii) use of full name and/or abbreviation for institutes (NCBI, EBI) and database (GEO); (iv) typos, spelling errors and other variation (e.g. database versus data bank).
Due to lack of Danish national identification numbers, four patients did not have their transfusion data registered in the Blood Bank database.
The study used data from the JPMC blood bank database.
The contig and unigene size distributions were consistent, which indicated that the Illumina sequencing solution was reproducible and reliable.> All of the unigenes were compared to the sequences in public databases, including NR, the Nucleic acid data bank (NT), Swiss-Prot, KEGG, COG, and GO database, using BLASTX with a cutoff e-value of 10−5 (Table 2).
Structural mapping of the active site residues was performed using Pymol [ 80]. aaRS: Aminoacyl tRNA synthetases; CDD: Conserved domains database; PDB: Protein data bank.
Examples of secondary tabular in vivo toxicity data are the Carcinogenic Potency Database (Gold et al. 2001), U.S. EPA IRIS reports, National Library of Medicine (NLM) TOXNET databases (Hazardous Substances Data Bank and Chemical Carcinogenesis Research Information System), and California EPA.
The E.U. money will fund four new projects: a database for information derived from "DNA arrays," which monitor the expression of thousands of genes at once; a data bank of three-dimensional protein structures; a database of biochemical interactions between proteins; and a project to integrate several existing EBI databases so that researchers can conduct more sweeping searches.
All auto-annotated peptidase genes identified were manually curated by performing BLAST analysis against apicomplexan genome sequence databases and against various protein databases [ 32] such as the protein data bank (PDB), Swiss-Prot and non-redundant (NR) protein sequence databases.
Despite more and more native structures are included in protein data bank (PDB) (Berman et al., 2000) database, the gap between the sequenced proteins and the native structures is still enlarging due to the exponential increase of protein sequences produced by large-scale genome and transcriptome sequencing.
