RAPHAEL - Data resource Precompiled sets

TRAINING AND TESTING SETS, Downloads and rankings:

• 35% sequence identity:
• 247 non-repeats: 294 CATH domains used for training and testing.
• 105 repeats: 104 CATH domains used for training and testing.
• Insertions: Residues assigned visually as periodic or not part of the periodicity.
• Repeat length: The repeating unit length assigned visually.

DISCOVERY SETS, Downloads and rankings:

• 35% sequence identity:
• Ranked CATH 3.4 domain list (SVM score≥0) All CATH domains with SVM scores greater than 0. Period matrix, JPEG pymol generated image and links to CATH. Useful for a quick visualization of the CATH 3.4 repeated domains. All domains sorted by highest SVM score to 0 (higher SVM score indicates higher periodicity). Redundancy reduction at S level (pairwise sequence identity ≤ 35%)
• CATH 3.4 domains (SVM score≥0) All CATH domains with SVM scores greater than 0. PDB and fasta files. Redundancy reduction at S level (pairwise sequence identity ≤ 35%)
• Ranked CATH 3.4 domain list (SVM score≥1) All CATH domains with SVM scores greater than 1. Period matrix, JPEG pymol generated image and links to CATH. Useful for a quick visualization of the CATH 3.4 repeated domains. All domains sorted by highest SVM score to 0 (higher SVM score indicates higher periodicity). Redundancy reduction at S level (pairwise sequence identity ≤ 35%)
• CATH 3.4 domains (SVM score≥1) All CATH domains with SVM scores greater than 1. PDB and fasta files. Redundancy reduction at S level (pairwise sequence identity ≤ 35%)

• 60% sequence identity:
• Ranked CATH 3.4 domain list (SVM score≥0) All CATH domains with SVM scores greater than 0. Period matrix, JPEG pymol generated image and links to CATH. Useful for a quick visualization of the CATH 3.4 repeated domains. All domains sorted by highest SVM score to 0 (higher SVM score indicates higher periodicity). Redundancy reduction at S level (pairwise sequence identity ≤ 60%)
• CATH 3.4 domains (SVM score≥0) All CATH domains with SVM scores greater than 0. PDB and fasta files. Redundancy reduction at S level (pairwise sequence identity ≤ 60%)
• Ranked CATH 3.4 domain list (SVM score≥1) All CATH domains with SVM scores greater than 1. Period matrix, JPEG pymol generated image and links to CATH. Useful for a quick visualization of the CATH 3.4 repeated domains. All domains sorted by highest SVM score to 0 (higher SVM score indicates higher periodicity). Redundancy reduction at S level (pairwise sequence identity ≤ 60%)
• CATH 3.4 domains (SVM score≥1) All CATH domains with SVM scores greater than 1. PDB and fasta files. Redundancy reduction at S level (pairwise sequence identity ≤ 60%)

• 40% sequence identity:
• Ranked PDB chains (SVM score≥0) All PDB chains with SVM scores greater than 0. Period matrix and JPEG pymol generated image. Useful for a quick visualization of the PDB repeated chains. All chains sorted by highest SVM score to 0 (higher SVM score indicates higher periodicity). Redundancy reduction at 40% using cd-hit.
• PDB chains (SVM score≥0) All CATH domains with SVM scores greater than 0. PDB and fasta files. Redundancy reduction at 40% using cd-hit.
• Ranked PDB chain list (SVM score≥1) All PDB chains with SVM scores greater than 1. Period matrix and JPEG pymol generated image. Useful for a quick visualization of the PDB repeated chains. All chains sorted by highest SVM score to 1 (higher SVM score indicates higher periodicity). Redundancy reduction at 40% using cd-hit.
• PDB chains (SVM score≥1) All PDB chains with SVM scores greater than 1. PDB and fasta files. Redundancy reduction at 40% using cd-hit.

Instructions:

$> cd wherever-you-downloaded-the-package

$> tar xvfz archive-name.tar.gz 

$> cd archive-name

If you encounter any problems using the downloaded test sets, please contact the author at silvio@cribi.unipd.it.