First of alll.... Thanks...... for ur reply.....

using ur code..... I was able to eliminate the redundancy....... But i was not able to get the whole data.... I got a fragmented data..... (Incomplete dataset returned)

I entered the data file as follows...

Data.txt 
>gi|49329899|gb|AAT60545.1| chitinase [Bacillus thuringiensis serovar 
+konkukian str. 97-27
MLNKFKFICCTLVIFLLLPLAPFQAQAANNLGSKLLVGYWHNFDNGTGIIKLRDVSPKWDVINVSFGETG
GDRSTVEFSPVYGTDAEFKSDISYLKSKGKKVVLSIGGQNGVVLLPDNAAKQRFINSIQSLIDKYGFDGI
 
>gi|49330053|gb|AAT60699.1| chitinase [Bacillus thuringiensis serovar 
+konkukian str. 97-27
MKSKKFTLLLLSLLLFLPLFLTNFITPNVVLADSQKQDQKIVGYFPSWGIYGRNYQVADIDASKLTHLNY
AFADICWNGKHGNPSTHPDNPNKQTWNCKESGVPLQNKEVPNGTLVLGEPWADVTKSYPGSGTTWEDCDK
 
>gi|49478343|ref|YP_037789.1| chitinase [Bacillus thuringiensis serova
+r konkukian str. 97-27]
MLNKFKFICCTLVIFLLLPLAPFQAQAANNLGSKLLVGYWHNFDNGTGIIKLRDVSPKWDVINVSFGETG
GDRSTVEFSPVYGTDAEFKSDISYLKSKGKKVVLSIGGQNGVVLLPDNAAKQRFINSIQSLIDKYGFDGI
 
>gi|49329899|gb|AAT60545.1| chitinase [Bacillus thuringiensis serovar 
+konkukian str. 97-27
MLNKFKFICCTLVIFLLLPLAPFQAQAANNLGSKLLVGYWHNFDNGTGIIKLRDVSPKWDVINVSFGETG
GDRSTVEFSPVYGTDAEFKSDISYLKSKGKKVVLSIGGQNGVVLLPDNAAKQRFINSIQSLIDKYGFDGI
 
>gi|49478497|ref|YP_034712.1| chitinase [Bacillus thuringiensis serova
+r konkukian str. 97-27]
MKSKKFTLLLLSLLLFLPLFLTNFITPNVVLADSQKQDQKIVGYFPSWGIYGRNYQVADIDASKLTHLNY
AFADICWNGKHGNPSTHPDNPNKQTWNCKESGVPLQNKEVPNGTLVLGEPWADVTKSYPGSGTTWEDCDK
YARCGNFGELKRLKAKYPHLKTIISVGGWTWSNRFSDMAADEKTRKVFADSTVDFLREYGFDGVDLDWEY

[download]
Using ur code i obtained the following result..... 
>gi|49329899|gb|AAT60545.1| chitinase [Bacillus thuringiensis serovar 
+konkukian str. 97-27
MLNKFKFICCTLVIFLLLPLAPFQAQAANNLGSKLLVGYWHNFDNGTGIIKLRDVSPKWDVINVSFGETG
+  

>gi|49330053|gb|AAT60699.1| chitinase [Bacillus thuringiensis serovar 
+konkukian str. 97-27

>gi|49478343|ref|YP_037789.1| chitinase [Bacillus thuringiensis serova
+r konkukian str. 97-27]

>gi|49478497|ref|YP_034712.1| chitinase [Bacillus thuringiensis serova
+r konkukian str. 97-27]

[download]
The result shows unique sequence...... but is not complete.. I require the complete data along with the two lines after the >gi....... (even the alphabets lines) 
MLNKFKFICCTLVIFLLLPLAPFQAQAANNLGSKLLVGYWHNFDNGTGIIKLRDVSPKWDVINVSFGETG
GDRSTVEFSPVYGTDAEFKSDISYLKSKGKKVVLSIGGQNGVVLLPDNAAKQRFINSIQSLIDKYGFDGI

[download]
thanks

In reply to Re^2: How to eliminate redundancy in huge dataset (1,000 - 10,000) by Kenin
in thread How to eliminate redundancy in huge dataset (1,000 - 10,000) by Kenin

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