Protein sequences submitting

Biological raw data are stored in public databanks (such as Genbank or EMBL for primary DNA sequences). The data can be submitted and accessed via the World Wide Web. Protein sequence databanks like trEMBL provide the most likely translation of all coding sequences in the EMBL databank. Sequence data are prominent, but also other data are stored, e.g.yeast two-hybrid screens, expression arrays, systematic gene-knock-out experiments, and metabolic pathways. 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

Another major source are the amino acid sequences direcdy derived from protein sequencing. Thousands of such sequences have been detected by the SWISS-PROT curators in publications (or have been directly submitted by researchers to SWISS-PROT) and entered into the database. Protein sequences detected by the NCBI journal scan have also been included. For some proteins the Brookhaven Protein Data Bank (PDB) (Abola et al., 1996) is the only source for the sequence information. The PDB entries are checked regularly, and new SWISS-PROT entries were created whenever necessary. 

Submit a protein sequence and you will receive secondary structure prediction via e-mail. 

Both the nucleic acid sequences and the protein sequences derived from the biological information are collected in most such databases. Large amounts of data in these databases need to be sorted, stored, retrieved, and analyzed. Selection of subsets of data for particular analysis should also be done. IT providers designed such a data warehouse and developed an interface that provides an important benefit to researchers by making it easy to access the existing information and also to submit new entries (i.e., datamining) (Table 5.6). Middlewares and structured query language (SQL) softwares were developed for this purposes. The former one is used... 

As an example, a protein sequence of a bacterial NADH oxidase, in this case the protein sequence of a water-forming NADH oxidase from Streptococcus mutans, is submitted to a blastp search ... 

The exon-intron database can be downloaded from EID at http //www.mcb.-harvard.edu/gilbert/EID/, whereas online database search can be conducted at Exlnt (http //intron.bic.mus.edu.sg/exint/exint.html). On the Exlnt home page, click Search Exlnt by keywords to open the query page. Choose Complete Exlnt for the Database, choose Text word for Search field, and enter the keyword (protein name, e.g., hexokinase, lysozyme). Click the Submit button to receive search results. The output includes locus name, description (viz. GenBank), NCBI ID and pointer (nucleotide sequence), phase and position of introns, number, size, and length (in amino acids) of exons, nucleotide position for the introns, and protein sequence... 

The method of Rost and Sander (Rost and Sander, 1993), which combines neural networks with multiple sequence alignments known as PHD, is available from the PredictProtein (Rost, 1996) server of Columbia University (http //cubic.bioc. columbia.edu/predictprotein/). This Web site offers the comprehensive protein sequence analysis and structure prediction (Figure 12.8). For the secondary structure prediction, choose Submit a protein sequence for prediction to open the submission form. Enter e-mail address, paste the sequence, choose options, and then click the... 

The PANAL/MetaFam server (http //mgd.ahc.umn.edu/panal/run panal.html) analyzes protein sequence for Prosite patterns, Prosite profiles, BLOCKS, PRINTS, and Pfam. Check the options, paste the query sequence, and click the Submit button. The analytical results are returned with a graphical sketch of the predicted features,... 

At your selected database site, follow links to the sequence comparison engine. Enter about 30 residues from the protein sequence in the appropriate search field and submit it for analysis. What does this analysis tell you about the identity of the protein ... 

With the exception of studies on bovine serum albumin (BSA) and human transferrin, all other digests were carried out on Coomassie Blue-stained gel bands that had been excised from SDS polyacrylamide gels and submitted in eppendorf tubes to the internal protein sequencing service of the HHMI Biopolymer Laboratory/W.M. Keck Foundation Biotechnology Resource Laboratory at Yale University (5). The BSA and transferrin samples were subjected to SDS-PAGE in the Keck Facility and were otherwise prepared as described (5). Proteins were quantified by subjecting 10-15% aliquots of all gel slices to hydrolysis and ion exchange amino acid analysis (5). 

These protein attributes are then submitted to a database search. This search identifies a protein by looking at the best match between experimental data and data obtained by in-silico processing and digestion of a protein sequence database. The identification and characterization procedures using bioinformatics tools will be the topic of Section 4.4. 

Brunei University, London David Jones On-line structure prediction service allows the user to submit a protein sequence, perform a prediction method of choice and receive the results of the prediction via e-mail. The user is permitted to select one of three prediction methods to apply to the sequence PSIPRED, MEMSAT 2 or GenTHREADER (http // insuUn.brunel.ac.uk/threader/threader.html), a new sequence profile-based fold recognition method http //insulin.brunel.ac.uk/psipred/... 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

In most cases, protein sequences come with a DNA sequence. There are some exceptions—people do sequence proteins directly—and such sequences must be submitted without a corresponding DNA sequence. SWISS-PROT presently is the best venue for these submissions. 

Because the majority of submissions contain a single nucleotide sequence and one or more coding region features (and their associated protein sequences), the functionality just outlined can frequently result in a finished record, ready to submit... 

The UniProt Archive (UniParc) provides a stable, comprehensive, nonredundant sequence collection by storing the complete body of publicly available protein sequence data. Although most protein sequence data are derived from the translation of DDBJ/EMBL/GenBank sequences, primary protein sequence data are also submitted directly to UniProt or derived from the PDB entries. The Archive also captures protein sequence data from other sources such as Ensemble, International Protein Index (IPI), NCBI-RefSeq, FlyBase, and WormBase. Each protein sequence is assigned to a unique UniParc identifier (UPI ) and represented only once in the Archive. In UniParc, the... 

The purpose of the molecular scanner is for the identification of proteins that were separated with a 2-DE gel. Therefore, for each scan point, the lists of peptide masses are submitted to the peptide mass fingerprint identification program Smartldent [51], which searches the protein sequence database SWISS-PROT and returns a list of matching proteins and their score. 

Sequencing facilities. There are a number of commercial facilities that offer protein sequencing services (see Note 4). Be sure to obtain their recommended protocol for sample preparation before submitting a fragment for analysis... 

A. Babajide, R. Farber, 1. L. Hofacker, J. Inman, A. S. Lapedes, and P. F. Stadler, Exploring protein sequence space using knowledge based potentials. J. Comp. Biol, submitted, Santa Fe Institute preprint 98-11-103 (1999). 

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