Geneious prime remove gaps
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“Annotate from Database” allows you to annotate your sequence with particular genes or motifs from a custom annotation database. Gaps (if allowed) are scored as the lowest value from the score matrix (e.g. Therefore the total score is 4+2+5=11 out of a maximum of 4+maximum(4,4)+5=13 for a percentage similarity of 85%. For example if one sequence is LLK and the other is LIK using the Blosum62 matrix, L/L scores 4, I/I scores 4, L/I scores 2, K/K scores 5. The percentage similarity is the sum of the similarity values for each position as a fraction of the sum of the maximum similarity values of the bases/residues in each position. Similarly, if contributing annotations have different qualifier values, the resulting qualifier value will consist of all contributing qualifier values sorted in order of decreasing similarity. All transferred annotations will be annotated with a “Transferred From” qualifier indicating the names of the sequences the annotation came from (sorted in order of decreasing similarity), and a “Transferred Similarity” qualifier which indicates the percentage similarity of the most similar sequence the annotation was transferred from.Īnnotations of the same type and covering the same interval that would be transferred from multiple sequences are merged together such that the name of the transferred annotation will consist of the names of all contributing annotations sorted in order of decreasing similarity.
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To set a sequence as a reference sequence Ctrl-click on it and choose ’Set as reference sequence’.Īnnotations will only be transferred where the annotated sequence and the reference/consensus sequence have at least the specified minimum similarity. This function can be accessed from the “Annotate and Predict” menu, or in the “Live Annotate and Predict” tab in the sequence viewer. Using Transfer Annotations, you can copy annotations to the reference and/or consensus sequence of an alignment or assembly. In each case, the annotation(s) will be copied across regardless of the similarity between the sequences. You can also use the associated options: “Copy all x to.” to copy all annotations of the currently selected annotation type on the selected sequence and “Copy all in selected region to.” to copy all annotations in the selected sequence. This will give you the option of either transferring the annotation to the consensus sequence, reference sequence (if there is one), or any of the other sequences in the alignment or assembly. You can copy annotations from one sequence to other sequences in the same alignment or assembly document by right-clicking on the annotation and choosing “Annotation” →“Copy to”. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.Up 8.1.3 Transferring annotations from other sequences While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges.
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A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. However, most of its populations started to decline a few millennia ago. The Eurasian lynx ( Lynx lynx) is one of the most widely distributed felids in the world.