Pairwise alignment results with the original coordinates.
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@charles-plessy-7857
Last seen 6 months ago
Japan

I am exploring genomic sequences in interactive mode and I align them pairwise using the pairwiseAlignment function from _Biostrings_, fed with sequences extracted by getSeq from _BSgenome_. Here is a toy example below (no biological relevance).

Is there an easy way to display the original coordinates in the output ?

> pairwiseAlignment(
+     getSeq(Scerevisiae, GRanges("chrI:100-120")),
+     getSeq(Scerevisiae, GRanges("chrI:250-270"))
+ ) |> writePairwiseAlignments()
########################################
# Program: Biostrings (version 2.62.0), a Bioconductor package
# Rundate: Mon Feb  7 01:49:32 2022
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: P1
# 2: S1
# Matrix: NA
# Gap_penalty: 14.0
# Extend_penalty: 4.0
#
# Length: 24
# Identity:      11/24 (45.8%)
# Similarity:    NA/24 (NA%)
# Gaps:           6/24 (25.0%)
# Score: -73.49569
#
#
#=======================================

P1                 1 GGCCA---ACCTGTCTCTCAACTT     21
                     | |||   |||   |  | | |  
S1                 1 G-CCACTTACCCTACCATTACC--     21


#---------------------------------------
#---------------------------------------

Instead of the above, I wish I had:

chrI             100 GGCCA---ACCTGTCTCTCAACTT     120
                     | |||   |||   |  | | |  
chrI             250 G-CCACTTACCCTACCATTACC--     270

That would help my brain a lot !

Biostrings Alignment • 643 views
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