Hi,

I was trying to use blast{BoSSA} to BLAST some sequences I have in a DNAbin
object, but it is taking too long and I am not sure it is working properly.

After running the example below the console returns several lines of "Read
2178 items" one after another and has been there for several mins.

Could you spot if I am doing something wrong or if this is normal?

Many thanks.

Example data:

```

x <- structure(c("55548", "43297", "35309", "34468",
"AATTCAATGCTCGGGAAGCAAGGAAAGCTGGGGACCAACTTCTCTTGGAGACATGAGCTTAGTGCAGTTAGATCGGAAGAGCA",
"AATTCCTAAAACACCAATCAAGTTGGTGTTGCTAATTTCAACACCAACTTGTTGATCTTCACGTTCACAACCGTCTTCACGTT",
"AATTCACCACCACCACTAGCATACCATCCACCTCCATCACCACCACCGGTTAAGATCGGAAGAGCACACTCTGAACTCCAGTC",
"AATTCTATTGGTCATCACAATGGTGGTCCGTGGCTCACGTGCGTTCCTTGTGCAGGTCAACAGGTCAAGTTAAGATCGGAAGA"),
.Dim = c(4L, 2L))

y <- t(sapply(strsplit(x[,2],""), tolower))
rownames(y) <- x[,1]

y<-as.DNAbin(y)

testblast<-blast(y, program="blastn", database= "nr", entrezquery=
"viridiplantae[organism]")

```



Thanks,

Alicia




-- 
Alicia Mastretta-Yanes
PhD student
Centre for Ecology, Evolution and Conservation
School of Biological Sciences
University of East Anglia
Norwich NR4 7TJ
ENGLAND

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