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Biological Integrated Knowledge Environment

Biological Integrated Knowledge Environment.

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Biological Integrated Knowledge Environment

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  1. Biological Integrated Knowledge Environment What follows is an illustration of how BioBIKE can solve interesting scientific problems that would be very difficult for the nonprogramming biologist to approach in any other way. The example uses BioBIKE's graphical programming language, which is under development. However, every operation is already possible using the text-base language, which you can access from http::/ramsites.net/~biobike This demonstration is best viewed as a slide show.To do this, click Slide Show on the top tool bar, then View show. Click to move on to the next slide.

  2. What Defines Cyanobacteria? Cyanobacteria comprise an ancient and coherent group of organisms that happen to look alike (at least to our eyes). In fact, the genetic diversity of cyanobacteria greatly exceeds that of vertebrates, a group we consider as consisting of very different creatures. Amidst the difference, what makes cyanobacteria cyanobacteria?

  3. What Defines Cyanobacteria? Another way to put this question is:What genes are in common amongstall cyanobacteria? By analyzing the functions of these genes, we may deduce the characteristics that unite cyanobacteria.

  4. Pallette Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice We'll use BioBIKE to accomplish the following tasks: - Define a set of protein common to all cyanobacteria - Examine this set to discern core cyanobacterial functionsThe first set is to define a set, so click the Definition button in the Pallete. Results Expand History

  5. Pallette APPLY-FUNCTION– Applies a function to a list of valuesASSIGN – Sets a variable to a given value DEFINE – Sets for the first time a variable to a given value DEFINE-FUNCTION – Defines operation of a new functionMY-FUNCTIONS – Lists functions you have defind MY-VARIABLES – Lists variables you have defined SWAP – Gives x's value to y and y's value to x Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice Clicking Definition brings up a menu related to defining sets, variables, and functions.Click the green triangle next to Define (Clicking Define itself would bring up a description of the function). Results Expand History

  6. Pallette Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS variable name value A function box appears, with internal boxes telling you what the function needs. Click on the first entry box to provide the name of the set you're defining. Results Expand History

  7. Pallette Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins value The box becomes selected (outlined in red). Type in the box the name of the set (or for now, just click).Then click on the value box, where you'll provide the definition of the set. Results Expand History

  8. Pallette Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins value You want to define this set as all protein common to all cyanobacterial genomes. Click the Genomes button in the Pallette to bring up functions that work on genomes. Results Expand History

  9. Pallette Auto Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output CHROMOSOME-OF- Returns chromosome' s frameCODING-GENES-OF- Returns those genes that encode proteinsCOMMON-ORTHOLOGS-OF- Returns orthologs common to all organisms in the given listDOWNSTREAM-SEQUENCES-OF- UndocumentedGENES-OF- Returns the gene of given organism, replicon, gene, proteinINTERGENIC-SEQUENCES-OF - Returns sequences between genes of an organismNICKNAMES-OF- Returns nicknames of given organismNONCODING-GENES-OF- Returns those genes that do not encode proteinsORGANISM-OF- Returns organism's framePROTEINS-OF- Returns proteins' framesREPLICON-OF- Returns chromosome, replicon (plasmid) or contig's frameSEQUENCE-OF- Returns the sequence of the given gene, protein, contig, replicon, or genomeUPSTREAM-SEQUENCES-OF- Returns sequences upstream of a set of genes Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins COMMON-ORTHOLOGS-OF sounds promising ("orthologs" are, in brief, those proteins related by common evolutionary descent). You could find out more by clicking on the function, but for now, click on the triangle next to the function. Results Expand History

  10. Pallette all-cyanobacteriafilamentous-cyanobacteriaheterocystous-cyanobacteriamarine-cyanobacteriaunicellular-cyanobacteria COMMON-ORTHOLOGS-OF set of organisms Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins The function fills the definition hole and, as before, tells you what it needs to know in order to function. Click on the green down arrow to see appropriate choices. Common orthologs amongst all-cyanobacteria is what you want, so click on that. Results Expand History

  11. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins The definition seems to be complete, so click the rightward green GO triangle next to define to accomplish the task. Results Expand History

  12. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins The result appears in the Results window below. Evidently there are 744 proteins in common amongst cyanobacteria (they're listed in terms of the protein of Anabaena PCC 7120). But what are they? To find the descrip-tions of these proteins click the Genes/Proteins button in the Pallette. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  13. Pallette Description-analysis – Properties of genes and proteins Gene-Neighborhood – Genes/sequences around a given gene or coordinate Translation – Codon amino acid conversions and properties of amino acids Gene-protein-types – Type checks related to genes and proteins COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins You're given four categories of choices. Description-analysis looks like the most likely choice, so click the green GO triangle next to that. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  14. Pallette Description-analysis – Properties of genes and proteins Gene-Neighborhood – Genes/sequences around a given gene or coordinate Translation – Codon amino acid conversions and properties of amino acids Gene-protein-types – Type checks related to genes and proteins COG-ID-OF - Returns the COG ID of given gene or protein DESCRIPTION-OF - Returns best description of given gene[s] or protein[s] GENE-DESCRIBED-BY - Returns gene annotated as given GENE-NAMED - Converts string name into gene frame GENE-OF - Returns the gene of given organism, replicon, gene, protein HYDROPHOBICITY-OF - Returns hydrophobicity score for amino acids LENGTH-OF - Returns the length of a given entity LENGTHS-OF - Returns the length of each entity in a list of entities MW-OF - Calculates molecular weight of amino acid sequence ORTHOLOG-OF – Returns phylogenetically related gene or protein PROTEIN-OF - Returns protwib of given organism, replicon, gene, protein SEQUENCE-OF - Returns the sequence of the given entity COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins Good guess! That got me to DESCRIPTION-OF, which seems very likely to do what you want. Click the green GO triangle next to that. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  15. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF entity The usual function box appears. You could type in the name of your set, core-proteins, but you might misspell it. Click on the downward green arrow to get appropriate choices to put in the entity box. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  16. Pallette (specific gene)(previous result)core-proteins COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF entity Sets and variables you've previously defined appear as appropriate choices. Click on core-proteins. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  17. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF core-proteins You could execute the function now (clicking the GO triangle), but this will get you just the descriptions. You'd like them labeled with the protein name. Click on the white/green MORE arrow in the upper right corner to see what optional capabilities the function supports. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  18. Pallette LABELED COMMON-ORTHOLOGS-OF all-cyanobacteria LENGTH Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF core-proteins Labeling is evidently one of the options. Click on LABELED. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  19. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins That's all you want to specify for the descriptions, so click on the right GO triangle to get the result. Results Expand RESULT 1: A7120.p-All0004A7120.p-All0005A7120.p-All0006A7120.p-All0007A7120.p-All0008A7120.p-Asl0009A7120.p-All0010A7120.p-All0011A7120.p-Alr0033 A7120.p-All0036A7120.p-Alr0044A7120.p-Alr0045...(744) History

  20. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins The result appears in the Result window,… at least part of it. To see the whole thing, click on RESULT 2. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  21. Pallette Result 2 A7120.p-All0004 "ATP synthase subunit gamma" A7120.p-All0005 "ATP synthase subunit alpha" A7120.p-All0006 "ATP synthase subunit delta" A7120.p-All0007 "ATP synthase subunit b" A7120.p-All0008 "ATP synthase subunit b" A7120.p-Asl0009 "ATP synthase subunit c" A7120.p-All0010 "ATP synthase subunit a" A7120.p-All0011 "ATP synthase subunit 1" A7120.p-Alr0033 "DHNA phythltransferase" A7120.p-All0036 "UDP-N-acetylmuramoylalanyl-D-g A7120.p-Alr0044 "hypothetical protein" A7120.p-Alr0045 "hypothetical protein" A7120.p-All0049 "DNA mismatch repair protein" A7120.p-Alr0051 "IMP dehydrogenase" A7120.p-Alr0052 "thioredoxin" A7120.p-Alr0063 "ribosome binding factor A" A7120.p-All0082 "riboflavin biosynthesis protei A7120.p-Alr0088 "single-stranded DNA-binding pr A7120.p-Alr0094 "glutamate racemase" A7120.p-Alr0096 "solanesyl diphosphate synthase A7120.p-All0109 "photosystem I subunit III prec A7120.p-Alr0110 "sialoglycoprotease" A7120.p-Alr0115 "N5-glutamine methyltransferase A7120.p-Alr0116 "hypothetical protein" COMMON-ORTHOLOGS-OF all-cyanobacteria Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins You can use the scroll bar of the result window to scroll through all of the descriptions, but even with what you see right now, certain things stand out. First, many of the descriptions are of expected proteins (e.g. ATP synthase). But you see two that are surprising: "hypothetical protein" (click to continue). Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  22. Pallette Result 2 A7120.p-All0004 "ATP synthase subunit gamma" A7120.p-All0005 "ATP synthase subunit alpha" A7120.p-All0006 "ATP synthase subunit delta" A7120.p-All0007 "ATP synthase subunit b" A7120.p-All0008 "ATP synthase subunit b" A7120.p-Asl0009 "ATP synthase subunit c" A7120.p-All0010 "ATP synthase subunit a" A7120.p-All0011 "ATP synthase subunit 1" A7120.p-Alr0033 "DHNA phythltransferase" A7120.p-All0036 "UDP-N-acetylmuramoylalanyl-D-g A7120.p-Alr0044 "hypothetical protein" A7120.p-Alr0045 "hypothetical protein" A7120.p-All0049 "DNA mismatch repair protein" A7120.p-Alr0051 "IMP dehydrogenase" A7120.p-Alr0052 "thioredoxin" A7120.p-Alr0063 "ribosome binding factor A" A7120.p-All0082 "riboflavin biosynthesis protei A7120.p-Alr0088 "single-stranded DNA-binding pr A7120.p-Alr0094 "glutamate racemase" A7120.p-Alr0096 "solanesyl diphosphate synthase A7120.p-All0109 "photosystem I subunit III prec A7120.p-Alr0110 "sialoglycoprotease" A7120.p-Alr0115 "N5-glutamine methyltransferase A7120.p-Alr0116 "hypothetical protein" COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins Hypothetical protein? Proteins possessed by cyanobacteria separated perhaps by over two million years of evolution must have critical functions. Seeing this result, you've decided to change course and identify all core proteins annotated "hypothetical". Perhaps we can learn the most from them. Click the white/red X to leave the Result window. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  23. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins To look for those highly conserved hypothetical proteins, you need to search for the words "hypothetical protein" in the descriptions. The descriptions are strings (collections of letters and other characters). So click on the String/Sequences button of the pallette. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  24. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria String-analysis - Functions that analyze the properties of strings String-extraction - Functions that deliver parts of strings String-production - Functions that manipulate and produce strings String-type-checks - Functions that determine the type of a string Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins String-analysis looks good. Click on its GO triangle to find a function that might work to identify "hypothetical protein" in the descriptions. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  25. Pallette ALIGNMENT-OF– Aligns sequences via Clustal ALPHABET-OF – Returns the minimal string of characters contained in string COUNT-OF - Returns the number of times the query appears in the target COUNTS-OF – Returns the number of times the query(s) appear in the target(s) LENGTH-OF – Returns the length of a given entity LENGTHS-OF – Returns the length of each entity in a list of entities MATCH-OF – Searches target for first instance of query MATCHES-OF – Searches target for all instances of query COMMON-ORTHOLOGS-OF all-cyanobacteria String-analysis - Functions that analyze the properties of strings String-extraction - Functions that deliver parts of strings String-production - Functions that manipulate and produce strings String-type-checks - Functions that determine the type of a string Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins MATCHES-OF seems perfect. Click on the GO triangle next to it. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  26. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins value or category MATCHES-OF MATCHES-OF calls for something to match. Click on the down triangle to see perhaps appropriate choices. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  27. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria NOT EACH-OF PATTERNPATTERNS ENZYME ENZYMES PROPERTY PROPERTIES (specific entity)(previous result)core-proteins Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins value or category MATCHES-OF The function can find various kinds of matches – patterns, restriction sites, etc. But "hypothetical protein" is not on the list. You'll have to type it in yourself. X out of the box. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  28. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins MATCHES-OF Type "hypothetical protein" (click for this to be done automatically. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  29. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins pothetical protein” MATCHES-OF You need to specify where to look for these words. Click on the right green MORE arrow to extend the choices of this function. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  30. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria IN-EACH IN Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins “hypothetical protein” MATCHES-OF Choose IN-EACH, because you are looking not for "hypothetical protein" in the list of results but rather for those words within each of the individual subresults. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  31. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria (specific entity)(previous result)core-proteins Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins “hypothetical protein” value MATCHES-OF IN-EACH Click the green MENU triangle in the value box to get a list of appropriate choices. Then, choose previous result. Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  32. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins “hypothetical protein” previous result MATCHES-OF IN-EACH That seems to describe what you want to do, so click the green GO arrow to the left of MATCHES-OF Results Expand RESULT 2: ((A7120.p-All0004 "ATP synthase subunit gamma") (A7120.p-All0005 "ATP synthase subunit alpha") (A7120.p-All0006 "ATP synthase subunit delta")...(744) History

  33. Pallette COMMON-ORTHOLOGS-OF all-cyanobacteria Help Analysis Arithmetic Definition Genes/Proteins Genomes Input/Output Other Lists/Sets Logic String/Sequences Tables Favorites Exit Workspace Click a button above to choose a function. Press Help for general and specific advice DEFINE AS core-proteins DESCRIPTIONS-OF LABELED core-proteins “hypothetical protein” previous result MATCHES-OF IN-EACH The result window gives you a list of those proteins that are conserved amongst all cyanobacteria and are currently annotated as "hypothetical". You've gotten your wish and can consider each carefully to try to find clues as to their functions… later. For now click the Exit button in the pallette). Results Expand RESULT 3: ((A7120.p-Alr0044 hypothetical protein) (A7120.p-Alr0045 hypothetical protein) (A7120.p-Alr0116 hypothetical protein) ...(196) History

  34. Biological Integrated Knowledge Environment This example illustrated: - The power of an integrated knowledge environment You didn't need to read in any data or worry about formats. It was all there for you. - The power of a language that knows the concepts of biology You didn't need to teach the language the concept of "ortholog". This and many other biological concepts are built in. - The power of a graphical interface You were programming a computer. It wasn't that challenging. - The power of creative programming in solving biological problems You didn't use a premade program but examined each intermediate result as you went. This enabled you to see an unexpected and fascinating result that would have passed you by if you got only the final result. BioBIKE may be accessed from ramsites.net/~biobike

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