LYC project

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LYC project

Transcriptome Assembling

integrate gene set with cufflinks

mapping reads on genome with tophat

Genome Assembling

Close gaps

GapCloser from SOAP2denovo

Build scaffolds

Do not choose the best N50 (containing more linking errors)

Use SSPACE

Based trimed reads (36 x 2) from both PE and MP libraries

Build contigs

choose the best N50

Test on a broad range of K-mers

Do not apply pairing

Use ABySS

Based on reads from PE libraries

Reads cleaning

K-mer correction

Delete PCR duplicates

Trim adaptor contamination

Based on quality score

Sequencing

transcriptome

muscle

egg

liver

genomic DNA

mp libraries

9k

5k

3k

pe libraries

600 bp

300 bp

Evolution analyses

positive selection

run GO for the PSGs, relate them with some environmental factors

evolution speed

draw Ka/Ks ratio graph between lyc and another fish

run comel on the single copy gene families

gene families

GO/Pathway analyses

based on the CAFE results

family expansion/contraction

run CAFE to get the expansion/contraction

run modeltest and mrbayes to get the overal phylogenetic tree

get single copy families

draw venn diagram

based on the ortholog groups

treefam method

ortholog groups

draw ortholog groups

run 'treebest nj' to infer orthlog relations

run 'treebest best' on the cds for each cluster

get the cds seqs for the protein multi-alignment

run muscle to get multi-alignment

get protein seqs for each cluster

call gene clusters

run hcluster_sg

wublastp

compute edge weight (g1*g2)/max(g1,g2)

use solar combine gene-to-gene blastp score

blastp the db sequences to itself

Database preparation

together with lyc proteins, build wublast db

download 6 fishes protein sequences from ensemble

Annotation

maker pipeline

add transcriptome data

use ensembl results as a start point

ensembl pipeline

integration

similarity search

based on uniprot vertebrate proteins

based on online LYC est

raw compute

others

ab inito prediction

repeat masking