Static data for KVL PigEST resource Version 1.0.1 (January 2007)

The following static data are available

• cDNA_names.html:
  Table of the libraries generated within the Sino-Danish project.

• hk_candidates.html:
  A list of gene clusters ranked according to the number of cDNA libraries they are expressed in. All gene clusters (1358) present in more than 30 libraries are shown.

• cDNA_spec_genes.html:
  A list of genes, where each gene are expressed much more in one cDNA library than in others.

• snp_candidates.html:
  Contains a list of putative SNPs. All SNPs are supported by at least two ESTs and present in more than 2 % of the ESTs covering that particular position of a cluster. Multiple SNPs might be present at a given position, see eg. Ss1.1-Utr1-UTR010049E05.5 around position 1080. Here two distinct variations are present ('C-------C----C----------' and 'C-----------'). This means that the variations are linked. That is, two distinct possible variations are found in the data, one ('C-----------') has a C instead of a T, but is otherwise identical to the consensus, the other contains C's at positions 1, 9, and 14 instead of the relevant consensus bases. This also show that every EST that has the C substitutions at position 1 and 9, also has the substitution at position 14.

  If a 12-mer word has more than 4 bases where it's different from the consensus, all 12 bases are reported. An example of this is Ss1.1-rova027_e10.5 (around position 300, SNP '-----A----------------TGCAGGAAAACCAA'), where a phylogenetic variant has an 'A' substitution (at postion 306), but further along larger variations. Looking at the EST-sequences you can see that this is due to both base substitutions and indels, therefore setting this variant apart from a classic SNP.

• gene_lib_profiles_thres_2.clean.tbl.gz:
  Expression profile for all genes and libraries. Rows represent genes, columns represent cDNA libraries. Only when a gene has at least two reads represented for a given library a value is given. Data are normalized column-wise, but not for rows allowing the user to extract subtables and normalize rows for each such subtable.

• ncRNA_candidates_M0_M1_clean.fasta:
  The non-coding RNA candidate list. As mentioned in the supplementary material of paper listed in the introduction some contigs and singletons match the same ncRNAs. All are indicated in this file, but check what you need/want.
• cluster_seqs.fasta.gz:
  fasta file of cluster consensus sequences. [A few sequences contain gaps which can appear in areas of weak consensus - often in larger clusters at a 'thin' section. Otherwise the cluster should be fine.]

• singleton_seqs.fasta.gz:
  fasta file of singleton sequences.

• EST_sequences_pub.fasta.gz:
  The raw 398837 public available EST sequences (as of Feb 17, 2005) from GenBank, EST division using the search term: "Sus scrofa[ORGN] AND gbdiv_est[PROP]". The sequences are named according to their accessions. In addition the clone, sequence end and library are indicated.

• EST_sequences_SD_raw.fasta.gz:
  The raw 823871 SD (Sino-Danish) EST sequences. These were obtained from a larger set of traces files using the phred with options -trim_alt "" -trim_cutoff 0.01. The sequences are named according to their clone names.

• EST_sequences_SD_raw.fasta.qual.gz:
  The quality file of EST_sequences_SD_raw.fasta.gz. Names correspond to the those in the fasta file.

• BLAST files: A file blastdb.tar can be made from
  blastdb.tar.part_0:
  blastdb.tar.part_1:
  blastdb.tar.part_2:
  blastdb.tar.part_3:
  blastdb.tar.part_4:
  In structions are given in blast_readme.txt: An archive that contains (gzipped) blast data for clusters and singletons matched against UniProt, Rfam (full), RNAdb, fantom and mirbase (7.0). As we for these RAW data used very relaxed parameters these data are HUGE: 4.3 GB (compressed). [Data was later processed (see the reference listed below).]

• SQL tables: The SQL tables from the distiller server. They are described in sqltables_readme.txt and can be found as sqltables.tar.

Miscellaneous

1. Web interface for assembly available at http://pigest.kvl.dk.
2. Details about data can also be found in the paper (and supp material):
   Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. J. Gorodkin et al., submitted.