Text version of summary for searching 2-7-13

2015-01-13

azim58 - Text version of summary for searching 2-7-13

Random Hexamer cDNA Library Sequence Summary
2-7-13

Control Liver Library Summary

Name (clone) size (bp) BLAST match Query Coverage E-value Max Identity
Database
L1 none
L2 229 Mouse DNA sequence from clone RP23-391P24 on chromosome 2,
complete sequence 99% 2.00E-111 99% nr nt
L3 Plasmid vector pFKm4, complete sequence
L4 Plasmid vector pFKm4, complete sequence
L5 Mus musculus papillary renal cell carcinoma (translocation-associated)
(Prcc), mRNA
L6 none
L7 Plasmid vector pFKm4, complete sequence
L8 none
L9 none
L10 Plasmid vector pFKm4, complete sequence

How many sequences were mostly all As with a very short sequence after
the As?
"5/10"

How many sequences did not sequence well and are therefore likely poly A
sequences (the plasmid vector pFKm4 sequences)?
"4/10"

How many sequences matched a mouse sequence?
"1/10"

Tumor Library Summary

Name (clone) size BLAST match Query Coverage E-value Max Identity Database
T1 23 none
T2 23 none
T3 103 Mus musculus BAC clone RP24-463C3 from 3, complete sequence 96%
2.00E-47 100% nr nt
T4 23 none
T5 23 none
T6 157 Mus musculus interferon regulatory factor 2 binding protein 2
(Irf2bp2), mRNA 96% 2.00E-75 100% mouse RefSeq RNA
T7 23
T8 23
T9 416 Mus musculus lysosomal-associated protein transmembrane 5
(Laptm5), mRNA 99% 0 100% mouse RefSeq RNA
T10 23

short poly A sequences
"7/10"

mouse sequences
"3/10"

Position of Sequences Relative to Transcript

Only two sequences from the tumor library align with mouse RNAseq
transcript sequences. The other mouse sequences align with genomic
sequences, but not known RNA sequences. These RNAseq sequences do not
just align to the 3’ end which is one of the aspects I was trying to
avoid when we decided to make the random hexamer library so this is good.

Tumor Library Sequence 6

Tumor Library Sequence 9

azim58wiki: