TY  - JOUR
A1  - Taron, Ulrike H.
A1  - Lell, Moritz
A1  - Barlow, Axel
A1  - Paijmans, Johanna L. A.
T1  - Testing of Alignment Parameters for Ancient Samples
BT  - Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool
JF  - Genese
N2  - High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.
KW  - ancient DNA
KW  - short-read mapping
KW  - palaeogenomics
KW  - paleogenomics
KW  - alignment sensitivity/specificity
Y1  - 2018
U6  - https://doi.org/10.3390/genes9030157
SN  - 2073-4425
VL  - 9
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Hofreiter, Michael
A1  - Hartmann, Stefanie
T1  - Reconstructing protein-coding sequences from ancient DNA
JF  - Odorant binding and chemosensory proteins
N2  - Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.
KW  - re-sequencing
KW  - mapping
KW  - genome assembly
KW  - targeted assembly
KW  - SRAssembler
KW  - ancient DNA
KW  - reference sequence
KW  - paleogenomics
Y1  - 2020
SN  - 978-0-12-821157-1
U6  - https://doi.org/10.1016/bs.mie.2020.05.008
SN  - 0076-6879
VL  - 642
SP  - 21
EP  - 33
PB  - Academic Press,  an imprint of Elsevier
CY  - Cambridge, MA.
ER  - 
TY  - JOUR
A1  - Palkopoulou, Eleftheria
A1  - Lipson, Mark
A1  - Mallick, Swapan
A1  - Nielsen, Svend
A1  - Rohland, Nadin
A1  - Baleka, Sina Isabelle
A1  - Karpinski, Emil
A1  - Ivancevici, Atma M.
A1  - Thu-Hien To, 
A1  - Kortschak, Daniel
A1  - Raison, Joy M.
A1  - Qu, Zhipeng
A1  - Chin, Tat-Jun
A1  - Alt, Kurt W.
A1  - Claesson, Stefan
A1  - Dalen, Love
A1  - MacPhee, Ross D. E.
A1  - Meller, Harald
A1  - Rocar, Alfred L.
A1  - Ryder, Oliver A.
A1  - Heiman, David
A1  - Young, Sarah
A1  - Breen, Matthew
A1  - Williams, Christina
A1  - Aken, Bronwen L.
A1  - Ruffier, Magali
A1  - Karlsson, Elinor
A1  - Johnson, Jeremy
A1  - Di Palma, Federica
A1  - Alfoldi, Jessica
A1  - Adelsoni, David L.
A1  - Mailund, Thomas
A1  - Munch, Kasper
A1  - Lindblad-Toh, Kerstin
A1  - Hofreiter, Michael
A1  - Poinar, Hendrik
A1  - Reich, David
T1  - A comprehensive genomic history of extinct and living elephants
JF  - Proceedings of the National Academy of Sciences of the United States of America
KW  - paleogenomics
KW  - elephantid evolution
KW  - mammoth
KW  - admixture
KW  - species divergence
Y1  - 2018
U6  - https://doi.org/10.1073/pnas.1720554115
SN  - 0027-8424
VL  - 115
IS  - 11
SP  - E2566
EP  - E2574
PB  - National Acad. of Sciences
CY  - Washington
ER  -