Revised 15/04/2005

README for Inparanoid Eukaryotic Ortholog Groups data download directory
********************************************************************************
This a description of the download directory of the Inparanoid website. For more 
information on how to use the Inparanoid program as well as the online tool 
please go to "http://inparanoid.cgb.ki.se/ehelp.html"
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A -	Main Inparanoid section using Ensembl and other datasets
-----------------------------------------------------------------------------

All files can be downloaded from http://inparanoid.cgb.ki.se/download/


----
Original fasta files:
Location; http://inparanoid.cgb.ki.se/download/current/sequences/processed/
---
processed fasta files:
Location; http://inparanoid.cgb.ki.se/download/current/sequences/processed/

Species files and their fasta files abbreviated as follows:
--------------------------------------------
Name	Species

ensAG   Anopheles gambiae (Ensembl)
ensAM   Apis mellifera (Ensembl)
ensCE   Caenorhabditis elegans (Ensembl)
ensCF   Canis familiaris (Ensembl)
ensDM   Drosophila melanogaster (Ensembl)
ensDR   Danio rerio (Ensembl)
ensFR   Fugu rubripes (Ensembl)
ensGG   Gallus gallus (Ensembl)
ensHS   Homo sapiens (Ensembl)
ensMM   Mus musculus (Ensembl)
ensPT   Pan troglodytes (Ensembl)
ensRN   Rattus norvegicus (Ensembl)
ensTN   Tetraodon nigroviridis (Ensembl)
modCB   Caenorhabditis briggsae (Model organism database)
modCE   Caenorhabditis elegans (Model organism database)
modDD   Dictyostelium discoideum (Model organism database)
modDM   Drosophila melanogaster (Model organism database)
modDP   Drosophila pseudoobscura (Model organism database)
modMM   Mus musculus (Model organism database)
modOG   Oryza sativa (Model organism database)
modRR   Rattus norvegicus (Model organism database)
modSC   Saccharomyces cerevisiae (Model organism database)
modSP   Schizosaccharomyces pombe (Model organism database)
ncbAT   Arabidopsis thaliana (NCBI)
ncbEC   Escherichia coli (NCBI)
sanPF   Plasmodium falciparum (Sanger)

FASTA	Combined fasta file containing all the above species
		(FASTA.phr/FASTA.pin/FASTA.psq can be used in combination
		 to create a local blast library )





SQL tables used to construct the main Inparanoid Database
location; 
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Name				Description

sqltable_full		Table of all Ensembl proteins used;
				Each column represents:
				1 - Gene identifier
				2 - Transcript identifier
				3 - Peptide identifier 
				4 - External database identifier, e.g. HUGO.
				5 - Uniprot acc no.
				6 - Ensembl Family identifier
				7 - Ensembl Family description
				8 - Gene/Protein description
				9 - Species abbreviation (see fasta list above)
                                9 - Original fasta filename:Original fasta header

Main section Inparanoid clustering results:
----------------------------------------------------

Name				Description


orthologs.?????-?????.html	Output files containing all Inparanoid clusters for
				each species pair in html format. See species fasta
				file list above for species abbreviations.
				e.g. orthologs.ensHS-ensDM.html; All Inparanoid
				clusters between Homo sapiens and Drosophila
				melanogaster.
				Location:
				http://inparanoid.cgb.ki.se/download/current/html/


orthologs.?????-?????.xml      Output files containing all Inparanoid clusters for
                                each species pair in html format. See species fasta
                                file list above for species abbreviations.
                                e.g. orthologs.ensHS-ensDM.html; All Inparanoid
                                clusters between Homo sapiens and Drosophila
                                melanogaster.
				
				Contains the most info of all result files. Contains 
				internal description.

                                Location:
                                http://inparanoid.cgb.ki.se/download/current/xml/




sqltable.?????-?????		Output files containing all Inparanoid clusters for
				each species pair in table format. See species fasta
				file list above for species abbreviations.
				e.g. sqltable.ensHS-ensCE; All Inparanoid
				clusters between Homo sapiens and Caenorhabditis
				elegans
				Each column represents:
				1 - Cluster number
				2 - Seed ortholog-pair blast score in bits
				3 - Species abbreviation
				4 - Inparanoid score
				5 - Protein identifier
                                6 - Bottstrap value for seed inparalog/ortholog
				Location:
				http://inparanoid.cgb.ki.se/download/current/sqltables/

longsqltable.?????-?????        Output files containing all Inparanoid clusters for
                                each species pair in table format. See species fasta
                                file list above for species abbreviations.
                                e.g. sqltable.ensHS-ensCE; All Inparanoid
                                clusters between Homo sapiens and Caenorhabditis
                                elegans
                                Each column represents:
                                1 - Cluster number
                                2 - Seed ortholog-pair blast score in bits
                                3 - Species abbreviation
                                4 - Inparanoid score
                                5 - Protein identifier
				6 - Bottstrap value for seed inparalog/ortholog
				7 - Description/name
				8 - Original fasta filename:Original fasta header
				9 - External ID
                                Location:
                                http://inparanoid.cgb.ki.se/download/current/sqltables/