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README file for isoforms.txt 

isoforms.txt contains descriptions of canonical and alternative isoforms of 
refseq-coding genes, utilizing an overloaded header line.

The basic format of the fasta descriptor is as follows:

> (ISOFORM ID) exons{...} spl{...} aspl{...} ptc{...}

ISOFORM ID:
	a few examples : NM_000120-CDS.canonical
			 NM_000029-CDS.alt-isoform-1
			 NM_000098-CDS.alt-isoform-1.NMD-CANDIDATE
			 NM_000066-CDS.alt-fragment-2
			 NM_000036-CDS.alt-fragment-1.NMD-CANDIDATE

The isoform id consists of up to three indicators fields:
	1) RefSeq identifier followed by '-CDS' to indicate that only the 
	   coding region is described.
		ex: NM_000120-CDS 

	2) canonical-seq - indicates that the corresponding isoform is 
	   spliced identically to the canonical refseq entry.
		ex: canonical-seq

	  	or 

	   alt-isoform-# - indicates that the entry is the #th alternative
	   isoform of the refseq-coding gene of interest.	
	   	ex: alt-isoform-1

		or 

	   alt-fragment-# - indicates that entry is the #th alternative isoform
	   of the refseq-coding gene of interest _and_ that the reading frame
	   for this isoform could not be determined unambigiously (i.e. the
	   most 5' exon of this isoform does not overlap with a coding exon of 
	   the RefSeq gene)
		ex: alt-fragment-2

	3) The first two fields are followed by '.NMD-CANDIDATE' if the isoform
 	   was found to contain a premature termination codon.

exons field:
	contains the number of exons in the isoform followed by a colon and 
	the exon boundaries in parenthesis, where the range of an exon is 
	indicated by a '-' between coordinates and the range of an intron is 
	indiacted by a '.' between coordinates.

		ex:
		exons{19:(1-100.1066-1194.2043-2171.3413-3552.3851-3928.4012-4090.4628-4753.5126-5210.5323-5424.6024-6108.6383-6556.6986-7055.7218-7328.7706-7919.9147-9280.10943-11031.11183-11266.11930-12016.12377-12424)}

spl field:
	contains the number of splice sites in the isoform followed by a colon
	and a two field descriptor of the splice site.
		ex: 
		spl{3:(REF-E|152.3776,PS1.C|3856.13072,REF-E|14376.16321)} aspl{1:(PS1.C|3856.13072:1)}

	splice descriptors and their meanings:

		REF	
			canonical splice in canonical RefSeq isoform

		REF-E	
			canonical splice in alternative isoform

		REF-S	
			splice that aligned within 7 nt of the actual 
			position of the canonical splice, most likely as a 
			result of poor alignments around the splice boundary.
			these are not thought to be indicative of alternative
			splicing.

		PS(#)
			a perfect skip alternative splice 
			# indicates the number of exons of the canonical isoform
			that are skipped

		
		ALT-(3|5|R)D(3|5|R)A
			alternative splice with a single alternative splice 
			site and a canonical site
				3 and 5 indicate that the alternative donor 
				or acceptor is either 3' or 5' of the 
				corresponding canonical splice donor or 
				acceptor  
				R indicates that the alternative donor or 
				acceptor matches the canonical donor or acceptor
		
		CON-(3|5|R)D(3|5|R)A
			alternative splice with two alternative splice sites

		EINC-(3|5|R)D(3|5|R)A
			exon inclusion (complete new exon is added from intron
					sequence in the canonical isoform)

		Trailing ".C's or ".N"'s indicate:
				.C : the splice site following the alternative 
				     splice is covered by ESTs
				or

				.N : the splice site following the alternative 
				     splice is covered by ESTs

	The coordinates of splice donor and acceptor sites are listed 
		"donor"."acceptor"
		ex: 389.13072


aspl field:
		this field is identical to the spl field except that only
		alternative (and not canonical) splices are described.
		in addition, the number of ESTs covering the alternative splice
		sites is listed.

			ex:  aspl{1:(ALT-5DRA.C|66.2644:1)}

ptc field:
		this field has four pieces of information separated by commas

			1) coordinate of premature termination codon in 
			   translated amino acid sequence

			2) the number of splice pairs beyond the premature 
			   termination codon that are covered by ESTs

			3) splice descriptor corresponding to the alternative
			   splice that introduces the premature termination
			   codon

			4) number of ESTs covering the splice that introduces
			   the premature termination codon		
		

			ex: ptc{210,5,ALT-RD3A.C,1}

* note that isoform that do not contain premature termination codons will have 
  an empty ptc field and canonical isoforms will have an empty aspl field
 
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