Sequence records

Seven representative Mossbauer spectra are presented. The five spectra of Figure 1 are a sequence recorded following various treatments of sample 1, the fully hydroxylated sample. Spectrum 1A was recorded at liquid nitrogen temperature after Fe(C0)5 hac been admitted to the sample cell. This is essentially a spectrum of frozen Fe(C0)5. Spectrum IB was recorded at room temperature after the sample had been heated to 350 K for 10 hours. This spectrum consists of two components a zero-valent iron species (34%) and an Fe + species (66%). The numbers in parentheses represent the fraction of the total spectral area produced by the... 

The protein sequence databases are the most comprehensive source of information on proteins. The goal of this chapter is to describe the different protein sequence databases available to researchers. It is necessary to distinguish between universal databases that cover proteins from all species and specialized data collections that store information about specific families or groups of proteins, or about the proteins of a specific organism. Two categories of universal protein sequence databases can be discerned simple archives of sequence data and annotated databases in which additional information has been added to the sequence record. The next section describes the Protein Information Resource (PIR), the oldest protein sequence database SWISS-PROT, an annotated universal sequence database and TrEMBL, the supplement of... 

Metalliferous sediments are a common component of modern ocean-floor sedimentary sequences, recording halos of metal dispersion from seafloor hydro-thermal vent systems (Gurvich, 2006). Sulfidic black shales are also commonly present as intercalations in ancient subaqueous volcanic sequences, where each likely represents a significant hiatus in volcanic activity and deposition. These shale horizons form geophysical anomalies (conductors) that are routinely drilled during exploration for volcanogenic massive sulfide (VMS) base metal deposits. 

Welcome to O fflLl, Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBL the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources atNCBI and elsewhere. 

Protein and nucleic acid sequences are submitted electronically to the United States Patent and Trademark Office (USPTO) to avoid the introduction of errors in printed documents and to simplify the job of examining patent claims that include biosequences. Short sequence listings are printable in the USPTO s full text database, but for longer sequences the electronic sequence records are stored in the Publication Site for Issued and Published Sequences (PSIPS), located at http // seqdata.uspto.gov/. 

In this picture of cytochrome evolution, point mutations occur at random along the DNA which codes for the amino acid sequence, and the protein produced from this mutated DNA is tested in the organism for its ability to operate as a functioning cytochrome. If the molecule is impaired, then the mutation is deleterious, and if the molecule is ineffective, the mutation is lethal. We never see these lethal mutations in the sequence record because the unfortunate carriers of them are weeded out. Residues such as histidine-18 and methionine-80 are absolutely essential. 

Figure 7.3.11 Schematic experimental arrangement for differential pulse polarography. For clarity, this diagram shows the functions as they would be organized in separate electronic stages in a free-standing DPP unit. In contemporary instruments, a computer performs many of the roles delineated here, including sequencing, recording of data, calculation of difference signals, and display of results.

An example of a stopped-flow measurement with TCSPC is shown in Fig. 5.38. A sequence recorded for a single flow-stop is shown left. The result accumulated over 500 stops is shown right. 

Fig. 5.53 20 steps of a TOF sequence recorded at an adult human head by TCSPC memory swapping. Acquisition time 100 ms per curve, ADC resolution 1,024 channels. Diode laser 785 nm, 2.5 mW, detector H5773-20. Left Source-detector distance 8 cm, count rate 1.8T0 s. Right Source-detector distance 5 cm, count rate 4.5T0 s ... 

Fig. 5.125 Bursts of single molecules. Part of a longer sequence recorded by sequencer-controlled memory swapping. 1 ms per step of the sequence, 64 ADC channels...

Recently, the members of the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ) introduced a better sequence identifier, one that combines an accession (which identifies a particular sequence record) with a version number (which tracks changes to the sequence itself). It is expected that this kind of Seq-id will become the preferred method of citing sequences. 

Because the components of a Seq-aimot have specific references to locations on Bioseqs, the Seq-annot can stand alone or be exchanged with other scientists, and it need not reside in a sequence record. The scope of descriptors, on the other hand, does depend on where they are packaged. Thus, information about Bioseqs can be created, exchanged, and compared independently of the Bioseq itself. This is an important attribute of the Seq-annot and of the NCBl data model. 

A sequence record for a gene and its protein product will typically have a single BioSomce descriptor at the Nuc-prot set level. A population or phylogenetic study, however, will have BioSource descriptors for each component. (The components can be nucleotide Bioseqs or they can themselves be Nuc-prot sets.) The BioSources in a population study will have the same organism name and usually will be distinguished from each other by modifier information, such as strain or clone name. 

GenBank presents a DNA-centered view of a sequence record. (GenPept presents the equivalent protein-centered view.) To maintain compatibility with these historical views, some mappings are performed between features on different sequences or between overlapping features on the same sequence. 

The Source Feature. The source feature is the only feature that must be present on all GenBank records. All features have a series of legal qualifiers, some of which are mandatory (e.g., /organism for source). All DNA sequence records have some origin, even if synthetic in the extreme case. In most cases, there will be a single source feature, and it will contain the /organism. Flere is what we have in the example from Appendix 3.1 ... 

DNA sequence records from the public databases (DDBJ/EMBL/GenBank) are essential components of computational analysis in molecular biology. The sequence records are also reagents for improved curated resources like LocusLink (see Chapter... 

The submission process is governed by an international, collaborative agreement. Sequences submitted to any one of the three databases participating in this collaboration will appear in the other two databases within a few days of their release to the public. Sequence records are then distributed worldwide by various user groups and centers, including those that reformat the records for use within their own suites of programs and databases. Thus, by submitting a sequence to only one of the three major databases, researchers can quickly disseminate their sequence data and avoid the possibility that redimdant records will be archived. 

The Sequence Format form asks for the type of submission (single sequence, segmented sequence, or population, phylogenetic, or mutation study). For the last three types of submission, which involve comparative studies on related sequences, the format in which the data will be entered also can be indicated. The default is FASTA format (or raw sequence), but various contiguous and interleaved formats (e.g., PHYLIP, NEXUS, PAUP, and FASTA+ GAP) are also supported. These latter formats contain alignment information, and this is stored in the sequence record. 

Figure 4.1. Viewing a sequence record with Sequin. The sequence record viewer uses GenBank format, by default. In this example, a CDS feature has been clicked, as indicated by the bar next to its paragraph. Double-clicking on a paragraph will launch an editor for the feature, descriptor, or sequence that was selected. The viewer can be duplicated, and multiple viewers can show the same record in different formats.

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