NCBI - Blastn for CD-14 gene: (NR database)
<ws=wordsize, E=expected value, LC=low complexity, HRF=human repeat filter> |
| NR_Blastn_ws11_E10_LCon_HRFoff.gif |
| NR_Blastn_ws11_E8_LCon_HRFoff.gif |
E-value: |
- E=10, expect to find 10 matches out of the resulting matches by chance
- E=8, expect to find 8 matches out of the resulting matches by chance |
| NR_Blastn_ws15_E10_LCon_HRFoff.gif |
Wordsize: |
- longer wordsize match longer region (global match) --> faster
- shorter wordsize match shorter region (local match) --> slower |
| NR_Blastn_ws11_E10_LCoff_HRFoff.gif |
Low complexity:
|
- ON: eliminate statistically significant but biologically uninteresting reports from the blast output by masking these unwanted regions.
- OFF:
the uninteresting regions are not taken in to consideration and hence the alignment score might be biased. |
| NR_Blastn_ws11_E10_LCon_HRFon.gif |
| |
NCBI - Blastp for CD-14 gene: (NR database)
<ws=wordsize, E=expected value, LC=low complexity> |
| NR_Blastp_ws3_E10_LCon.gif |
| NR_Blastp_ws3_E7_LCon.gif |
| NR_Blastp_ws2_E10_LCon.gif |
| NR_Blastp_ws3_E10_LCoff.gif |
| |
| EST - Human database |
| NCBI - Blastn (EST-Human database) : EST_blastn_ws11_E10_LCon_HRFoff.gif |
| NCBI - tBlastn (EST-Human database) : EST_tblastn_ws3_E10_LCon.gif |
NR database: |
All GenBank, RefSeq, Nucleotides, EMBL, DDBJ, PDB sequences.
--> does not contain EST or STS sequences |
EST database: |
Human GenBank, EMB, DDBJ sequences from the EST Genbank database |
| |
| EMBnet |
| EMBnet - blastn (EST+HTC database) : EMBnet_blastn.jpg |
| EMBnet - blastp (trest database) : EMBnet_blastp.jpg |
TrEST: |
Trest is a database of protein sequences derived from ESTs sequencing data (human, mouse, rat, zebra fish, drosophila, cow, arabidobsis).
The ESTs are clustered, contigs are generated from the clusters by an unpublished procedure and translated. Trest entries are NOT real protein sequences (provided to find UniGene clusters), therefore we should be aware while using it since it can not be 100% trustworthy.
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