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Summary

Tag	transcripts_tomato/transcripts_sol
Owner	CAB Group
Input	BAC sequences from `seq`
Output	GenomeThreader based analysis of tomato/other solanaceae ESTs, in GFF3 format

This analysis runs the GenomeThreader program versus the BAC sequences, reporting the GenomeThreader output into GFF3.

Input

GenomeThreader is used to create splice-alignments of each EST versus the S.lycopersicum BAC sequences that are made available in the GFF3 format.

We filtered out alignments with 98% identity and 95% coverage for both tomato species and other solanaceae (as announced by e-mail on the 22 Jan 2007 to sol-bioinformatics, itag and to the sol-steering).

The GFF3 format is validated by the online GMOD service available at: http://www.gmod.org/gff3.[[BR]] The BAC GenBank id was used for naming each GFF3 file, as reported in the following examples:
BACGenBankid.transcripts_tomato.itag000.batch001.v1.gff3
BACGenBankid.transcripts_sol.itag000.batch001.v1.gff3
for the itag pipeline 000 and for the bach file 001.

Two GFF3 files for each BAC sequence in the submission, respectively described spliced alignments of tomato and other Solanaceae ESTs, named as:

<acc>.<ver>.transcripts_tomato.spliced_alignment.itag<pipever>.batch<batchnum>.v<ver>.gff3

<acc>.<ver>.transcripts_sol.spliced_alignment.itag<pipever>.batch<batchnum>.v<ver>.gff3

EST sequences are downloaded from the dbEST division of GenBank (current release is updated to October 2008). Up to now, sequences from different sources are available:
TOMATO:
- SOLLC = Solanum lycopersicum;
- SOLHA = Solanum habrochaites;
- SOLPN = Solanum pennellii;
- SOLLP = Solanum lycopersicum X Solanum pimpinellifolium;
OTHER_SOLANACEAE:
- SOLTU = Solanum tuberosum;
- SOLCH = Solanum chacoense;
- CAPAN = Capsicum annuum;
- CAPCH = Capsicum chinense;
- TOBAC = Nicotiana tabacum;
- NICBE = Nicotiana benthamiana;
- NICSY = Nicotiana sylvestris;
- NICAT = Nicotiana attenuata;
- NICLS = Nicotiana langsdorffii x Nicotiana sandera;
- PETHY = Petunia x hybrida;
OTHER_RELATED_SPECIES (RUBIACEAE):
- COFCA = Coffea canephora;
- COFAR = Coffea arabica;
Each dataset of EST sequences is processed as follows:
- Vector contaminations are trimmed using RepeatMasker for the detection and the masking of vectors using the NCBI's Vector database (update October 2008).
- Low complexity sub-sequences and simple repeats are masked using RepeatMasker Vector cleaned and masked ESTs for each dataset are spliced-aligned versus the S.lycopersicum BAC sequences.

EST to BAC alignments are released to the SGN repository as requested according to the BAC BATCH files.

Deletions are marked like this.	Additions are marked like this.
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. We filtered out alignments with 95% identity and 90% coverage for both tomato species and other solanaceae (as announced by e-mail on the 22 Jan 2007 to sol-bioinformatics, itag and to the sol-steering).	. We filtered out alignments with 98% identity and 95% coverage for both tomato species and other solanaceae (as announced by e-mail on the 22 Jan 2007 to sol-bioinformatics, itag and to the sol-steering).