Analysis Of The Distribution Of Developmental Gene Transcripts In The Intact Body Of The Annelids Pygospio elegans, Platynereis dumerilii And Arenicola marina
This repository is contain the results of a project conducted at the Bioinformatics Institute, aimed to determine the distribution of transcripts coding developmental genes in three annelid species with different regenerative abilities.
- Finding sequences containing homeobox domain(blastp)
- Annotation of selected sequences functionally and finding possible orthologs (eggnog mapper v.2.0.0)
- Conducting an phylogenetic analysis of possible orthologs (MAFFT v.7.526)
- Performing transcript distribution analysis (Python)
Phylo.ipynb
- the notebook contains code for constructing phylogenetic treesmain.ipynb
- the notebook contains steps of transcript distribution analysis: selection of transcripts according to annotation, code for constructing heatmaps
ANTP.fasta
,all_prot.fasta
,paired.fasta
- files contain sequences for alignment in fasta formatmafft.tree
,NKL.tre
- phylogenetic trees in Newick format for visualizationAmar_maNOG.emapper.annotations
,Pele_maNOG.emapper.annotations
,Pdum_maNOG.emapper.annotations
- eggNOG-mapper-annotated transcripts
my_tree.png
- visualization of the phylogenetic tree for all analyzed transcriptsDiffExp1.png
- hitmap of putative developmental genes found only in Pygospio elegansDiffExp2.png
- hitmap of putative developmental genes found in annelids with posterior regenerationDiffExp3.png
- hitmap of putative developmental genes found in all three annelids
- Possible candidate genes to explain anterior regeneration could be BARX1, GSC
- Possible candidate gene to explain posterior regenerationn could be caudal
Belikova Angelina
- BI studentElena Novikova
- supervisorMaxim Nesterenko
- supervisor
If you have any questions or suggestions regarding this work, feel free to adress via email: Belikova Angelina - [email protected]