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Topic: Subfamilies

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Linnaean taxonomy

	FunShift: a database of function shift analysis on protein subfamilies -- Abhiman and Sonnhammer 33 (Supplement 1): ...
		Subfamilies for the Pfam families were generated using the BETE
		a subfamily pair was predicted by using the percentage of CSS
		The Screenshot shows the markup of RSS (‘R’ symbol) and CSS (‘C’ symbol) for a subfamily pair from the SNARE domain family (Pfam: PF05739).
	nar.oxfordjournals.org /cgi/content/full/33/suppl_1/D197 (1717 words)

	Climate and the U.S. distribution of C4 grass subfamilies and decarboxylation variants of C4 photosynthesis -- Taub 87 ...
		Climate and the U.S. distribution of C4 grass subfamilies and decarboxylation variants of C4 photosynthesis -- Taub 87 (8): 1211 -- American Journal of Botany
		subfamilies with annual precipitation that was independent of
		The strongest relationships of grass subfamily and C
	www.amjbot.org /cgi/content/full/87/8/1211 (2225 words)

	FunShift: Database of Pfam Subfamilies and Functional Shift Analysis
		It is compilation of subfamilies derived from Pfam domain family database and the analysis of these subfamilies for functional conservation or divergence (functional shift).
		Subfamilies are frequently representative of sets of proteins with related functions and/or distinct domain organizations resulting from different evolution histories with in a Family.
		Function shift between a subfamily pair was predicted by using the percentage of CSS and RSS as variables in classification functions.
	funshift.cgb.ki.se /faq.html (869 words)

	[No title] (Site not responding. Last check: )
		We interpret the branching pattern as clustering into at least six subfamilies, designated A-F. The presence of highly similar elements within the B, C, D, and F subfamilies is evidence that a distinct progenitor has spawned each of these subfamilies.
		The nucleotide divergence between members of subfamily C was 5%-8%, suggesting that this subfamily has undergone a relatively recent burst of retrotransposition.
		The A and E subfamilies may have been spawned from ancestors of these four progenitors or from other, distinct progenitors.
	www.mnhn.fr /mnhn/oseb/these/resumes/vandergon.html (244 words)

	The mouse olfactory receptor gene family -- Godfrey et al. 101 (7): 2156 -- Proceedings of the National Academy of ...
		are encoded by genes at adjacent loci (5 subfamilies), or by
		The 150 subfamilies shared by the two species are indicated by pairs of red and green bars.
		Subfamilies unique to mouse or human, or found in both species, are indicated on the left.
	www.pnas.org /cgi/content/full/101/7/2156 (3960 words)

	RedNova News - Science - Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on ... (Site not responding. Last check: )
		Systematists have generally agreed on the composition of the subfamilies and to a certain extent on the number of the subfamilies, between 16 and 20.
		They found that the mole-rat subfamilies (Spalacinae and Rhizomyinae) were the sister group to all other muroids, but they were unable to resolve the branching pattern, among most of the remaining subfamilies and speculated that robust resolution may never be achieved.
		In all but four subfamilies, alternate topologies wherein they were not monophyletic could be rejected under either one or both optimality criteria at the 0.05 level (after Bonferroni correction to 0.0015 for Kishino-Hasegawa and Templeton's test).
	www.rednova.com /news/display?id=92552 (9123 words)

	Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily -- Riveros-Rosas et al. 270 (16): ... (Site not responding. Last check: )
		Subfamilies present only in one kingdom are indicated in italics: bacteria or archaea; normal type indicates subfamilies present in two or more kingdoms.
		Subfamilies with restricted distribution are shown in italics, with subfamilies with broad distribution shown in normal font.
		Identification of protein subfamilies as nonoverlapping clusters (closed groups) is advantageous over distance-based clustering methods because it is not necessary to set an arbitrary identity cutoff value, and permits the identification of both highly and poorly conserved groups of orthologous proteins.
	content.febsjournal.org /cgi/content/full/270/16/3309 (8680 words)

	Mosaic Structure and Retropositional Dynamics During Evolution of Subfamilies of Short Interspersed Elements in African ...
		) of the consensus sequences of the subfamilies
		Subfamilies of sequences are identified by differently colored backgrounds.
		Polytomies in the tree indicate the absence of a sufficient number of informative loci to support the corresponding relationships or the existence of incongruities with respect to patterns of insertion of SINEs among loci, possibly as a result of incomplete lineage sorting or interspecific hybridization (Takahashi et al.
	mbe.oxfordjournals.org /cgi/content/full/19/8/1303 (4936 words)

	Mydidae - Subfamilies (Site not responding. Last check: )
		He divided the family into three subfamilies on the basis of the shape of the aedeagus, i.e.
		In summarising the knowledge on the family Papavero and Wilcox (1974) proposed a new classification of the Mydidae dividing it into nine subfamilies.
		A preliminary classification in subfamilies, with the descriptions of two new genera from the Oriental and Australian regions.
	www.mydidae.tdvia.de /subfam.html (289 words)

	Classification of families and subfamilies of aquatic Coleoptera (beetles)
		Classification of families and subfamilies of aquatic Coleoptera (beetles)
		Classification of Families and Subfamilies of Aquatic Coleoptera
		Families and subfamilies of Coleoptera (with selectes genera, notes, references and data on family-group names, pp.
	www.inhs.uiuc.edu /cbd/waterbeetles/classification.html (58 words)

	Whole-genome analysis of Alu repeat elements reveals complex evolutionary history -- Price et al. 14 (11): 2245 -- ...
		Small subfamilies nested inside large subfamilies, a typical scenario in Alu repeat subfamilies, are not easily identified, because there is a tendency to split off a larger cluster (B) instead of identifying the nested subfamily (C).
		A timeline roughly depicting the average divergence of each subfamily from its consensus sequence and the approximate age obtained by applying a constant scaling factor of 4 million years per 1% divergence from consensus sequence are included at right.
		Batzer, M.A. and Deininger, P.L. A human-specific subfamily of Alu sequences.
	www.genome.org /cgi/content/full/14/11/2245 (4286 words)

	SUBFAMILIES HYDROBATINAE AND OCEANITINAE WITHIN THE FAMILY HYDROBATINAE
		Many classifications (e.g., Carboneras 1992c) divide the family into two subfamilies, Hydrobatinae and Oceanitinae, but this classification follows the AOU (1998) in not recognizing these until corroborated by multiple independent data sets that mark major, deep branches within the family.
		This provides strong support for the division of the Hydrobatidae into two subfamilies: Oceanitinae, comprising taxa from Oceanites oceanica to Fregetta tropica; and Hydrobatinae, with taxa from Hydrobates pelagicus to Oceanodroma castro.
		That the subfamilies Oceanitinae and Hydrobatinae be recognized with the family Hydrobatidae.
	www.museum.lsu.edu /~Remsen/SACCprop167.html (495 words)

	Australian River Assessment System: AusRivAS Protocols Development and Testing Report: Results (continued) (Site not responding. Last check: )
		For Queensland sites there was a distinct relationship between the number of chironomids picked from a sample and the number of chironomid subfamilies identified in the sample (Figure 9).
		Only one extra subfamily, Podonominae, was recorded and this occurred in a single edge habitat sample from an upland site from which 64 chironomids were collected using the minimum number of animals pick protocol.
		No extra subfamilies were collected in the extra 15 minutes of picking from any sample.
	www.deh.gov.au /water/rivers/nrhp/test/chapter4b.html (402 words)

	Guide to the Genera of New World Pleurostict Scarab Beetles (Site not responding. Last check: )
		The hierarchical level of families and subfamilies within the Scarabaeoidea is in disarray and remains unresolved.
		Whereas families, subfamilies, and tribes in the staphylinoids and curculionoids are being combined because of shared characters (thus increasing efficient data retrieval), the scarabaeoids are being split into numerous families because of supposed differences (thus, in our view, decreasing information retrieval).
		The position of the spiracles, however, is not a consistent character (Ritcher 1969), and, in recent years, subfamilies and tribes that were once included in the Laparosticti have been raised to higher taxonomic status (family and subfamily, respectively).
	www-museum.unl.edu /research/entomology/Guide/Scarabaeoidea/ScarabaeoideaO.htm (2302 words)

	DEAD box subfamilies (Site not responding. Last check: )
		Since homologies in flanking sequences are good indicators for the definition of subfamilies and since these homologies in general are reflected by high scores, this second criterium helps to confirm subfamilies.
		RNA stability, ribosome biogenesis; The p68 subfamily is best characterized by the p68 and related proteins.
		For the moment being, this is therefore considfered a subfamily.
	www.medecine.unige.ch /~linder/dead_box_subfamilies.html (1154 words)

	THREE SUBFAMILIES OF SHORT INTERSPERSED ELEMENTS OF THE DOG GENOME: POSSIBLE ORIGIN AND FUNCTIONS (Site not responding. Last check: )
		A multiple alignment showed that there are at least three subfamilies of SINE in the dog genome, differing point mutations, deletions and insertions.
		Age estimates were obtained from analysis of subfamily members divergence from consensus by using methodology as described by Britten [8], Kapitonov and Jurka [9].
		The average age of subfamily divergence was estimated as T=K/0.002 [8, 10].
	www.bionet.nsc.ru /bgrs/thesis/91 (1493 words)

	Untitled Document
		It can be hypothesised that if these subfamilies vary in their sensitivity to stimuli for performing specific tasks, such as fanning, this might result in some subfamilies carrying out those tasks more often than other subfamilies.
		Therefore it can be hypothesised that more genetically diverse colonies are more likely to accurately regulate the temperature in the hive than colonies with fewer subfamilies because they would have a larger distribution of temperature thresholds at which they would act to regulate brood nest temperature.
		In addition there was a significant difference between overall subfamily proportions in the colony and the proportion of subfamilies fanning at different temperatures.
	www.bio.usyd.edu.au /Social_InsectsLab/Julia/Julia.htm (356 words)

	Large-scale evaluation and prediction of function shift in protein families
		The methodology was evaluated in a large-scale test based on the Pfam database, from which we derived subfamilies with either the same or different EC numbers.
		Subfamilies were derived using the BETE method, which resulted in 997 subfamily pairs with four or more members per subfamily.
		We tested the hypothesis that the more CS and RS sites between two subfamilies, the more likely a functional shift between them is. The results showed a significant increase in CS and RS sites for subfamily comparisons with different EC numbers compared to cases with same EC numbers.
	www.iscb.org /ismb2004/posters/abhiman.saraswathiATcgb.ki.se_277.html (685 words)

	Three Tnt1 Subfamilies Show Different Stress-Associated Patterns of Expression in Tobacco. Consequences for ...
		B, Neighbor-joining tree obtained with an alignment of the 15 Tnt1 partial sequences obtained from cultured cells RNA (cul#) together with the consensus sequences for the Tnt1A (conA), Tnt1B (conB), and Tnt1C (conC) subfamilies.
		The 5.2-kb band corresponding to the Tnt1 genomic RNA is indicated by an arrow.
		of the Tnt1B subfamily (cul4) and Tnt1C (cul12) was amplified
	www.plantphysiol.org /cgi/content/full/127/1/212 (5390 words)

	Tips for keying ants: Subfamily (Site not responding. Last check: )
		The abdominal pedicle is made up of one or two segments, the petiole and postpetiole, that are between the thorax (the alitrunk) and the rest of the abdomen (the gaster).
		These subfamilies can also be differentiated by looking at the tips of their gasters.
		The Japanese Ant Database Group has a description of the abdominal pedicel and gaster region of ants with features diagnostic to subfamilies described and a database of ant images from several subfamilies.
	www.carleton.edu /curricular/resources/BIOL/ant/Subfamily.html (381 words)

	Conserved Subfamilies of the Drosophila HeT-A Telomere-Specific Retrotransposon -- Danilevskaya et al. 148 (1): 233 -- ...
		Conserved Subfamilies of the Drosophila HeT-A Telomere-Specific Retrotransposon -- Danilevskaya et al.
		The two subfamilies represented here are less different than the two shown in B. (D) Het-A44P is plotted against 1187 (2.2 kb).
		Analysis of sequences in the repetitive pattern shows that their similarity is mainly due to their A-rich nature.
	www.genetics.org /cgi/content/full/148/1/233 (4494 words)

	PANTHER - Classifications of Genes and Proteins
		The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
		Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms.
		For an increasing number of proteins, detailed biochemical interactions in canonical pathways are captured and can be viewed interactively.
	www.pantherdb.org (242 words)

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