Kluyveromyces lactis annotation database     annotation: please read carefully
	Getting started:
	PASS OVER AN ORF TO SELECT IT: orf name & annotation will appear in "ORF information" field. Click mouse on one of the following buttons to see if any result exists for this orf - "Hits in SwissProt" to see BLASTP result in SWISSPROT v41 - "Hits in sptrot+trEMBL nr" to see BLASTP result - "Hits in HmmPfam" to see HMMER motifs match in PFAM database - "Hits in KOG" to see best KOG match and KOG function prediction - "Paralogues" to see if any paralogs or duplicates - "Hits in Yeast" to see BLASTP result vs S. cerevisiae database (provided by Pasteur Institute) - "Hits in C. albicans" to see BLASTP result vs C. albicans database (Stanford University, assembly #6 ) - "Start Codons" gives a display of the first possible start codons (ATG,GTG, TTG) of an orf - "Element Upstream" displays an orf's upstream distribution of very small orfs (1 aa.and more). May be usfull for intron hunting. - "Run PSI-BLAST vs GenBank" to directly blast orf sequence at NCBI more to come soon ...
	Coloring schemes:
	The following coloring schemes are available to allow global display of similarity levels, coding probablity and domain patterns over entire regions of the chromosomes. They should be used as a guide to visualise and select ORFs for annotation. A more detailed "user guide" for this annotation database can be found here (yet to be written)
	COG function categories for genes are as determined at NCBI COGs
	J K L COG Functional categories D O M N P T R G C E F H I S NB: This coloring scheme applies to procaryotic (original COGs) . Eucaryal database (KOGs) is an extension to COGs. An updated version of this coloring scheme will be available soon
	BLASTP hits in SWISSPROT + trEMBL (May 2003 : sprot+trEMBL) Absolute cut-off expect limit for this set is P <= 1.0
	SwissProt+Trembl Blast Hits coloring High hit: P <= 1e -20 Medium hit : 1e -20 < P <=1e -05 Low hit : 1e -05 < P <=1.0  No hit Medium Hit  High Hit Low Hit
	BLASTP hits in SWISSPROT ( release 41.O) Absolute cut-off expect limit for this set is P <= 10.0
	SwissProt Blast Hits coloring High hit: P <= 1e -10  No hit Medium Hit Medium hit : 1e -10 < P <=1.0  High Hit Low Hit Low hit : 1.0 < P <=10.0
	BLASTP hits in S. cerevisiae protein set (Data provided by Institut Pasteur)
	S. cerevisiae Blast Hits coloring scheme High hit: P <= 1e -20  No hit Medium Hit Medium hit : 1e -20 < P <=1e -05  High Hit Low Hit Low hit : 1e -05 < P <=1.0
	BLASTP hits in C. albicans (1213 Contigs from the assembly #6 of Stanford University)
	C. albicans Blast Hits coloring scheme High hit: P <= 1e -20  No hit Medium Hit Medium hit : 1e -20 < P <=1e -05  High Hit Low Hit Low hit : 1e -05 < P <=1.0
	HMMER hits in PFAM DataBase
	Hmm PFAM Hits coloring High hit: P <= 1e -20  No hit Medium Hit Medium hit : 1e -20 < P <=1e -05  High Hit Low Hit Low hit : 1e -05 < P <=10.0
	GLIMMER 2.0 coding probability prediction
	Glimmer 2.0 Gene prediction coloring   Predicted gene Predicted gene / Overlapping problem
	K. lactis self matching BLASTP hits of
	Paralogs scheme coloring High is ≥ 8 copies Poor man's path to define paralogs:  A hit with a matched score ≥ 0.5 x(self matching) score and matched Expect ≥ 0.5 x (self matched Expect)  No paralogs Medium copy number Medium is ≥ 4 copies  High copy number Low copy number Low is ≥ 1 copy