================================= Project Summary --------------------------------- # Project Information Project Name : Pgenerosa_v071 Owner : kubu4 Create Date : 2019-07-10 12:30:24 # Project Properties Genus : Panopea Species : generosa Project Type : invertebrate Prefix : PGEN_ Common Name : Pacific geoduck Genetic Code : Standard Code # Input FASTA Filename : Pgenerosa_v071.fasta Filesize : 1.32 GB Number of Sequence : 14014 ================================= Job Information --------------------------------- # Official Gene Set >PASA Refinement - version : 2.3.3 - Transcripts FASTA file : Trinity.fasta # The source Job of the refinement job >Augustus-01 - version : 3.3.1 - Species : fly - Report genes on : both - Allowed gene structure : partial - cDNA (transcripts) sequences : Trinity.fasta - Protein sequences : 20180827_trinity_geoduck.fasta.transdecoder.fa # The consensus mask Job >Masked Repeat Consensus # The source jobs for consensus mask job >RepeatMasker >RepeatModeler # Family copy number summary Family Copy Numbers DNA 85 DNA/Academ 264 DNA/Crypton 200 DNA/Kolobok-T2 188 DNA/MuLE-MuDR 94 DNA/PIF-Harbinger 482 DNA/Sola 122 DNA/TcMar-Mariner 599 DNA/TcMar-Tc1 1266 DNA/hAT-Tip100 808 DNA/hAT-Tip100? 255 Type:DNA 4363 LINE 2153 LINE/CR1 4122 LINE/CR1-Zenon 1717 LINE/I-Nimb 72 LINE/Jockey 510 LINE/L1-Tx1 967 LINE/L2 1896 LINE/Penelope 735 LINE/Proto2 155 LINE/R2-Hero 211 LINE/RTE-X 2275 LINE/Tad1 97 Type:LINE 14910 Type:SINE 0 LTR/DIRS 192 LTR/Gypsy 1420 LTR/Ngaro 533 LTR/Pao 146 Type:LTR 2291 Type:EVERYTHING_TE 21564 Type:Simple_repeat 107 Type:Unknown 115322 # The functional Jobs on the OGS >BLAST protein vs protein (blastp)_SP01 - version : 2.7.1 - Protein Data Set : SwissProt - Maximum HSP Distinace : 30000 - Output type : tab - Matrix : BLOSUM62 - Expect : 1e-8 - Word Size : 3 - Gap Open : 11 - Gap Extend : 1 >DIAMOND Functional SP01 - version : 0.9.22 - Protein Data Set : SwissProt >BLAST protein vs protein (blastp) - version : 2.7.1 - Protein Data Set : 20180827_trinity_geoduck.fasta.transdecoder.fa - Maximum HSP Distinace : 30000 - Output type : tab - Matrix : BLOSUM62 - Expect : 1e-8 - Word Size : 3 - Gap Open : 11 - Gap Extend : 1 >DIAMOND Functional - version : 0.9.22 - Protein Data Set : 20180827_trinity_geoduck.fasta.transdecoder.fa >InterProScan - version : 5.29-68.0 >Pfam - version : 1.6 - E-value Sequence : 1 - E-value Domain : 10 >SignalP - version : 4.1 - Organism group : euk - Method : best - D-cutoff for SignalP-noTM networks : 0.45 - D-cutoff for SignalP-TM networks : 0.50 - Minimal predicted signal peptide length : 10 - Truncate to sequence length : 70