Bioinformatics

2. FBW 01-03-2012 Wim Van Criekinge RELOADED 2

5. 4 3 2 1 0 A brief history of time (BYA) Origin of life Origin of eukaryotes insects Fungi/animal Plant/animal Earliest fossils BYA

6. Rat versus mouse RBP Rat versus bacterial lipocalin

28. FEATURES Location/Qualifiers source 1..756 /organism="Listeria ivanovii" /strain="ATCC 19119" /db_xref="taxon:1638" RBS 95..100 /gene="sod" gene 95..746 /gene="sod" CDS 109..717 /gene="sod" /EC_number="1.15.1.1" /codon_start=1 /product="superoxide dismutase" /db_xref="PID:g44011" /db_xref="SWISS-PROT:P28763" /transl_table=11 /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKL NEAVSGHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPN GGGAPTGNLKAAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVS TANQDSPLSEGKTPVLGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRF DAAK" terminator 723..746 /gene="sod"

30. BASE COUNT 247 a 136 c 151 g 222 t ORIGIN 1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat 61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa 121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg 181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca 241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt 301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta 361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca 421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg 481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt 541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat 601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca 661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta 721 tcgaaaggct cacttaggtg ggtcttttta tttcta //

33. CC -!- FUNCTION: CYTOKINE WITH A WIDE VARIETY OF FUNCTIONS: IT CAN CC CAUSE CYTOLYSIS OF CERTAIN TUMOR CELL LINES, IT IS IMPLICATED CC IN THE INDUCTION OF CACHEXIA, IT IS A POTENT PYROGEN CAUSING CC FEVER BY DIRECT ACTION OR BY STIMULATION OF IL-1 SECRETION, IT CC CAN STIMULATE CELL PROLIFERATION & INDUCE CELL DIFFERENTIATION CC UNDER CERTAIN CONDITIONS. Comments CC -!- SUBUNIT: HOMOTRIMER. CC -!- SUBCELLULAR LOCATION: TYPE II MEMBRANE PROTEIN. ALSO EXISTS AS CC AN EXTRACELLULAR SOLUBLE FORM. CC -!- PTM: THE SOLUBLE FORM DERIVES FROM THE MEMBRANE FORM BY CC PROTEOLYTIC PROCESSING. CC -!- DISEASE: CACHEXIA ACCOMPANIES A VARIETY OF DISEASES, INCLUDING CC CANCER AND INFECTION, AND IS CHARACTERIZED BY GENERAL ILL CC HEALTH AND MALNUTRITION. CC -!- SIMILARITY: BELONGS TO THE TUMOR NECROSIS FACTOR FAMILY. DR EMBL; X02910; G37210; -. Database Cross-references DR EMBL; M16441; G339741; -. DR EMBL; X01394; G37220; -. DR EMBL; M10988; G339738; -. DR EMBL; M26331; G339764; -. DR EMBL; Z15026; G37212; -. DR PIR; B23784; QWHUN. DR PIR; A44189; A44189. DR PDB; 1TNF; 15-JAN-91. DR PDB; 2TUN; 31-JAN-94.

34. KW CYTOKINE; CYTOTOXIN; TRANSMEMBRANE; GLYCOPROTEIN; SIGNAL-ANCHOR; KW MYRISTYLATION; 3D-STRUCTURE. KeyWord FT PROPEP 1 76 Feature Table FT CHAIN 77 233 TUMOR NECROSIS FACTOR. FT TRANSMEM 36 56 SIGNAL-ANCHOR (TYPE-II PROTEIN). FT LIPID 19 19 MYRISTATE. FT LIPID 20 20 MYRISTATE. FT DISULFID 145 177 FT MUTAGEN 105 105 L->S: LOW ACTIVITY. FT MUTAGEN 108 108 R->W: BIOLOGICALLY INACTIVE. FT MUTAGEN 112 112 L->F: BIOLOGICALLY INACTIVE. FT MUTAGEN 162 162 S->F: BIOLOGICALLY INACTIVE. FT MUTAGEN 167 167 V->A,D: BIOLOGICALLY INACTIVE. FT MUTAGEN 222 222 E->K: BIOLOGICALLY INACTIVE. FT CONFLICT 63 63 F -> S (IN REF. 5). FT STRAND 89 93 FT TURN 99 100 FT TURN 109 110 FT STRAND 112 113 FT TURN 115 116 FT STRAND 118 119 FT STRAND 124 125

35. FT STRAND 130 143 FT STRAND 152 159 FT STRAND 166 170 FT STRAND 173 174 FT TURN 183 184 FT STRAND 189 202 FT TURN 204 205 FT STRAND 207 212 FT HELIX 215 217 FT STRAND 218 218 FT STRAND 227 232 SQ SEQUENCE 233 AA; 25644 MW; 666D7069 CRC32; MSTESMIRDV ELAEEALPKK TGGPQGSRRC LFLSLFSFLI VAGATTLFCL LHFGVIGPQR EEFPRDLSLI SPLAQAVRSS SRTPSDKPVA HVVANPQAEG QLQWLNRRAN ALLANGVELR DNQLVVPSEG LYLIYSQVLF KGQGCPSTHV LLTHTISRIA VSYQTKVNLL SAIKSPCQRE TPEGAEAKPW YEPIYLGGVF QLEKGDRLSA EINRPDYLDF AESGQVYFGI IAL //

37. PDB

38. PDB

39. PDB

40. PDB

41. Visualizing Structures Cn3D versie 4.0 (NCBI)

50. Relational Terminology ID NAME PHONE EMP_ID 201 Unisports 55-2066101 12 202 Simms Atheletics 81-20101 14 203 Delhi Sports 91-10351 14 204 Womansport 1-206-104-0103 11 Row (Tuple) Column (Attribute) CUSTOMER Table (Relation)

55. Example 3-tier model in biological database http://www.bioinformatics.be Example of different interface to the same back-end database (MySQL)

58. What is HTTP? In Summary : HTTP is an acronym for Hypertext Transfer Protocol. HTTP is the set of rules, or protocol, that enables hypertext data to be transferred from one computer to another, and is based on the client/server principle. Hypertext is text that is coded using the Hypertext Markup Language. These codes and HTTP work together to link resources to each other. HTTP enables users to retrieve a wide variety of resources such as text, graphics, sound, animation and other hypertext documents, and allows hypertext access to other Internet protocols.

60. What is HTML? HTML stands for Hypertext Markup Language. HTML consists of standardized codes, or "tags", that are used to define the structure of information on a web page. HTML is used to prepare documents for the World Wide Web. A web page is single a unit of information, often called a document, that is available on the World Wide Web. HTML defines several aspects of a web page including heading levels, bold, italics, images, paragraph breaks and hypertext links to other resources.

61. What is HTML? HTML is a sub-language of SGML, or Standard Generalized Markup Language. SGML is a system that defines and standardizes the structure of documents. Both SGML and HTML utilize descriptive markup to define the structure of an area of text. In general terms, descriptive markup does not specify a particular font or point size for an area of text. Instead, it describes an area of text as a heading or a caption, for example. Therefore, in HTML, text is marked as a heading, subheading, numbered list, bold, italic, etc.

62. What is a URL? URLs consist of letters, numbers, and punctuation. The basic structure of a URL is hierarchical, and the hierarchy moves from left to right: Examples: http://www.healthyway.com:8080/exercise/mtbike.html gopher://gopher.state.edu/ ftp://ftp.company.com/ protocol://server-name.domain-name.top-level domain:port/directory/filename

64. What is an IP Address? If you want to connect to another computer, transfer files to or from another computer, or send an e-mail message, you first need to know where the other computer is - you need the computer's "address." An IP (Internet Protocol) address is an identifier for a particular machine on a particular network; it is part of a scheme to identify computers on the Internet. IP addresses are also referred to as IP numbers and Internet addresses. An IP address consists of four sections separated by periods. Each section contains a number ranging from 0 to 255. Example = 198.41.0.52

65. What is an IP Address? The diagram below compares Class A, Class B and Class C IP addresses. The blue numbers represent the network and the red numbers represent hosts on the network. Therefore, a Class A network can support many more hosts than a Class C network.

66. What is Internet Addressing? Most computers on the Internet have a unique domain name. Special computers, called domain name servers, look up the domain name and match it to the corresponding IP address so that data can be properly routed to its destination on the Internet. An example domain name is: healthyway.com Domain names are easier for most people to relate to than a numeric IP address.

69. What is TCP/IP? TCP/IP stands for Transmission Control Protocol/Internet Protocol. TCP/IP is actually a collection of protocols, or rules, that govern the way data travels from one machine to another across networks. The Internet is based on TCP/IP.

71. What is TCP/IP? The relationship between data, IP, and networks is often compared to the relationship between a letter, its addressed envelope, and the postal system.

75. What is a packet? In addition to the actual data, packets also contain header information. The header of a packet contains both the originating and destination IP (Internet Protocol) address. The header also contains coding to handle transmission errors and keep packets flowing. Header information can be compared to addressing an envelope. Like the header of a packet, an envelope contains the addresses of both the sender and the recipient, in order to keep track of who the envelope is from and who it is going to.

76. What is a packet? Header information is used by routers to send packets across a network. Routers are computers that are dedicated to "reading" header information and determining which router to send the packet to next. Packets move from router to router until they reach their final destination, in much the same way that an envelope travels between postal substations before reaching the recipient. The packets that make up data, such as an e-mail message or a web page, will not necessarily all follow the same route to the final destination. The route that a packet travels depends on many variables, including network traffic at that particular moment and the size of the packet being sent.

77. What is a packet? Transmission Control Protocol/Internet Protocol (TCP/IP) is a set of rules that govern how data is transmitted across networks and the Internet. TCP/IP utilizes packets to send information across the Internet. TCP and IP have different functions related to packets.

80. What is a packet? The following diagram illustrates an e-mail message being sent across a network. 1. Data that makes up an e-mail message is split into packets by the IP portion of TCP/IP. IP also adds header information to each packet. 2. Using header information in the packets, routers determine the best path for each packet to take to its final destination. 3. The TCP portion of TCP/IP reassembles the packets in the correct order and ensures that all packets have arrived undamaged. Message is sent

81. What is Telnet? Telnet is a protocol, or set of rules, that enables one computer to connect to another computer. This process is also referred to as remote login. The user's computer, which initiates the connection, is referred to as the local computer, and the machine being connected to, which accepts the connection, is referred to as the remote, or host, computer. The remote computer can be physically located in the next room, the next town, or in another country.

82. What is Telnet? Once connected, the user's computer emulates the remote computer. When the user types in commands, they are executed on the remote computer. The user's monitor displays what is taking place on the remote computer during the telnet session. The procedure for connecting to a remote computer will depend on how your Internet access is set-up.

83. What is Telnet? Once a connection to a remote computer is made, instructions or menus may appear. Some remote machines may require a user to have an account on the machine, and may prompt users for a username and password. Many resources, such as library catalogs, are available via telnet without an account and password. Here is an example taken from a telnet session to Washington University in St. Louis, MO:

91. What is FTP? Anonymous FTP Anonymous FTP allows a user to access a wealth of publicly available information. No special account or password is needed. However, an anonymous FTP site will sometimes ask that users login with the name “anonymous” and use their e-mail address as the password.

93. What is FTP? Files on FTP servers are often compressed. Compression decreases file size. This enables more files to be stored on the server and makes file transfer times shorter. In order to use a compressed file it needs to be decompressed using appropriate software. It is a good idea to have current virus checking software on the computer before files are downloaded to it.

98. BioSQL